Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
All Classes All Packages

A

absolute() - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
AbsoluteValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
AbsoluteValue() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
 
accept(int) - Method in interface org.anchoranalysis.core.functional.checked.CheckedIntConsumer
 
accept(int, int) - Method in interface org.anchoranalysis.math.histogram.Histogram.BinConsumer
 
accept(int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.ScalarTwoDimensionalConsumer
Accepts a point like with a Consumer in general.
accept(int, int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.OffsettedScalarTwoDimensionalConsumer
Accepts a point
accept(int, int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.ScalarThreeDimensionalConsumer
Accepts a point like with a Consumer in general.
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
 
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
 
accept(ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition
 
accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
 
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.BeforeCondition
 
accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition
 
accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition
 
accept(ObjectMask, ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
 
accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
 
accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.CheckParsedFilePathBag
 
accept(Point2i) - Method in interface org.anchoranalysis.spatial.point.consumer.PointTwoDimensionalConsumer
Accepts a point like with a Consumer in general.
accept(Point2i, int) - Method in interface org.anchoranalysis.spatial.point.consumer.OffsettedPointTwoDimensionalConsumer
Accepts a point like with a Consumer in general.
accept(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedConsumer
 
accept(S, T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedBiConsumer
Calls the function
accepted() - Method in interface org.anchoranalysis.annotation.mark.DualMarks
The accepted marks.
acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in interface org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationConditon
 
acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationList
 
acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfAllHigh
 
acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfLowDisconnected
 
AcceptIterationConditon - Interface in org.anchoranalysis.image.voxel.object.morphological.accept
A condition that must be fulfilled for a particular iteration of a morphological operation to be accepted.
AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.accept
 
AcceptIterationList() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationList
 
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
 
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.BinaryKernel
 
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
 
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
 
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
This method is deliberately not broken into smaller pieces to avoid inlining.
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3
This method is deliberately not broken into smaller pieces to avoid inlining.
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3ZOnly
 
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.ErosionKernel3
This method is deliberately not broken into smaller pieces to avoid inlining.
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3
This method is deliberately not broken into smaller pieces to avoid inlining.
acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3NeighborMatchValue
This method is deliberately not broken into smaller pieces to avoid inlining.
acceptProposal(ToDoubleFunction<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
accepts(Class<?>) - Method in interface org.anchoranalysis.bean.initializable.property.PropertyDefiner
 
accepts(Class<?>) - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
 
acceptsAsSource(Class<?>) - Method in class org.anchoranalysis.bean.initializable.property.ExtractFromParam
Are the source-parameters acceptable for extraction? *
AccessObjectMask<T> - Interface in org.anchoranalysis.image.core.object.scale
Provides functions to provide access and creation to/from the object-mask representation of a generic type.
AccptProbCalculator<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
 
AccptProbCalculator(AnnealScheme, ExtractScoreSize<T>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.AccptProbCalculator
 
activateDebugMode(String) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
Activates debug-mode
add(double) - Method in class org.anchoranalysis.feature.energy.EnergyTotal
 
add(double) - Method in class org.anchoranalysis.plot.AxisLimits
 
add(double) - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
 
add(double, double, double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
add(int, int, int) - Method in class org.anchoranalysis.spatial.box.PointRange
 
add(int, long) - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
 
add(int, String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
 
add(int, RGBColor) - Method in class org.anchoranalysis.core.color.ColorList
 
add(int, UpdatableMarkSet) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
add(Color) - Method in class org.anchoranalysis.core.color.ColorList
 
add(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.task.InputTypesExpected
 
add(Double) - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
 
add(Exception) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
 
add(Exception) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
add(Exception) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
 
add(String) - Method in interface org.anchoranalysis.bean.StringBeanCollection
 
add(String) - Method in class org.anchoranalysis.bean.StringList
 
add(String) - Method in class org.anchoranalysis.bean.StringSet
 
add(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList
Adds a feature-name
add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
 
add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
 
add(String, boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
Adds a new output-name to the set of recorded names.
add(String, int) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex
Adds a new featureName and index
add(String, int) - Method in class org.anchoranalysis.overlay.OverlayProperties
 
add(String, String) - Method in class org.anchoranalysis.overlay.OverlayProperties
 
add(String, StoreSupplier<Stack>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
 
add(String, StoreSupplier<TimeSequence>) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
 
add(String, StoreSupplier<TimeSequence>) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
 
add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
 
add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
 
add(String, StoreSupplier<T>) - Method in interface org.anchoranalysis.core.identifier.provider.store.NamedProviderStore
 
add(String, StoreSupplier<T>) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap
Adds an entry to the map
add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
 
add(String, Feature<T>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
Adds a named-feature to the store.
add(String, Stack) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
 
add(String, Stack) - Method in class org.anchoranalysis.image.core.stack.NamedStacksUniformSize
 
add(String, Generator<T>) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
 
add(String, EnergyScheme) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
 
add(String, Mark) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
 
add(String, Mark) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
add(String, Mark) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
 
add(String, S, NamedProviderStore<D>, CheckedFunction<S, D, OperationFailedException>) - Static method in class org.anchoranalysis.bean.store.BeanStoreAdder
Adds an item a container (using a bridge) and explicitly specifying a new name
add(String, T) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
 
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
 
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
 
add(Optional<String>, String, S) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
Adds an item with an identifier
add(NamedBean<?>) - Method in class org.anchoranalysis.bean.define.Define
Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine a group where definitions are stored.
add(PermutationSetter) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterList
 
add(RGBColor) - Method in class org.anchoranalysis.core.color.ColorList
 
add(NameValue<T>) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
add(NamedProvider<T>) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
 
add(NameValueSet<T>) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
add(StatefulMessageLogger) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
 
add(SubmittedJob) - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
add(Feature<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
add(EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
add(ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVectorList
 
add(CacheTransferSource<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
 
add(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
add(Seed) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
add(Stack) - Method in class org.anchoranalysis.image.core.stack.TimeSequence
 
add(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
 
add(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannelsSimple
 
add(AcceptIterationConditon) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationList
 
add(ObjectMask) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
add(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
add(VoxelStatistics) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
 
add(VoxelsWrapper) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
 
add(MutableDirectory) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
 
add(FileType[]) - Method in class org.anchoranalysis.io.generator.ConcatenateFileTypes
 
add(OutputtedFile) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
 
add(OutputtedFile) - Method in class org.anchoranalysis.io.manifest.directory.Subdirectory
 
add(EnergySavedInd, VoxelizedMarkMemo, EnergyStackWithoutParams, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
add(MemoCollection, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
add(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
add(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
add(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
add(UpdatableMarkSet) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
add(MemoForIndex) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
add(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
 
add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
 
add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
add(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
add(CreateProposalVisualization) - Method in class org.anchoranalysis.mpp.proposer.visualization.CreateProposeVisualizationList
 
add(TerminationCondition) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
 
add(WeightedKernel<T>) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
 
add(AggregateReceiver<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
 
add(FeedbackReceiver<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
 
add(PeriodReceiver<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
 
add(IndexByRegion<T>) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
 
add(Overlay) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
add(Overlay, RGBColor) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
add(AnnotationGroup<T>) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
 
add(LevelResult) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
 
add(FileDetails) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
 
add(BoundingBox) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
add(BoundingBox, T) - Method in class org.anchoranalysis.spatial.rtree.RTree
Adds a bounding-box with a corresponding index.
add(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d
 
add(Point2i) - Method in class org.anchoranalysis.spatial.point.Point2d
 
add(Point2i) - Method in class org.anchoranalysis.spatial.point.Point2i
 
add(Point3i) - Method in class org.anchoranalysis.spatial.box.PointRange
 
add(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
add(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
add(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
add(S, T) - Method in interface org.anchoranalysis.plugin.image.task.grouped.AddToAggregateItem
 
add(T) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
Outputs an additional element in the sequence.
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
 
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer
Adds a element to the summary.
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
 
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
 
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
 
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
 
add(T, String) - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
 
add(T, S) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
Outputs an additional element in the sequence.
addAcceptedAnnotation(AssignmentOverlapFromPairs) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
 
addAcceptedAnnotation(T) - Method in interface org.anchoranalysis.plugin.annotation.comparison.AddAnnotation
 
addAcceptedAnnotation(T) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
addAcceptedAnnotation(T) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
 
addAdditionalOptions(Options) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
 
addAdditionalOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions
 
addAll(int, Collection<? extends UpdatableMarkSet>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
addAll(Collection<? extends ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
addAll(Collection<? extends UpdatableMarkSet>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
addAll(Collection<AnnotationGroup<T>>) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
 
addAll(Define) - Method in class org.anchoranalysis.bean.define.Define
Adds all the named-beans (shallow copy) from source to th ecurrent map
addAll(ColorList) - Method in class org.anchoranalysis.core.color.ColorList
 
addAll(FeatureList<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
addAll(ObjectCollection) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
addAll(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
addAll(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
addAll(MarkCollection, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
addAll(MemoForIndex) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
addAll(OverlayCollection) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
addAllOutputNamesTo(OutputEnabledMutable) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
Adds all possible output-names to a OutputEnabledMutable.
addAllScaled(ColorList, double) - Method in class org.anchoranalysis.core.color.ColorList
 
addAllToUpdatablePairList(ListUpdatableMarkSetCollection) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
AddAnnotation<T extends Assignment> - Interface in org.anchoranalysis.plugin.annotation.comparison
 
addBasicOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions
 
addBean(String, Object) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
 
addBean(String, Object) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
addBean(String, Object) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
 
addBeansFromList(Define, List<NamedBean<?>>) - Static method in class org.anchoranalysis.bean.define.adder.DefineAdderUtilities
 
addBlankChannel() - Method in class org.anchoranalysis.image.core.stack.Stack
 
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
 
addBoundChangeListener(BoundChangeListener) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncompleteDynamic
 
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
 
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
 
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
 
addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
 
addBuffer(FloatBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferFloat
 
addBuffer(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferByte
 
addBuffer(UnsignedIntBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferInt
 
addBuffer(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferShort
 
addBuffer(T, T) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
 
addChangeID(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
addChangeID(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
addChannel(Channel) - Method in class org.anchoranalysis.image.core.stack.Stack
 
addChannel(Channel) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
addChannelsFrom(Stack) - Method in class org.anchoranalysis.image.core.stack.Stack
 
AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
AddConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
 
AddConstantTo<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
AddConstantTo() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
 
AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria
Add Criteria
AddCriteriaDistanceTo - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
 
AddCriteriaDistanceTo() - Constructor for class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
 
AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria
 
AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
 
AddCriteriaFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
 
AddCriteriaFeatureRelationThreshold() - Constructor for class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
 
AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
 
AddCriteriaNever() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
 
AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria
 
AddCriteriaOr() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
 
AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria
 
AddCriteriaPair() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
 
addCustomNames(FeatureList<?>) - Method in class org.anchoranalysis.feature.name.FeatureNameList
Add the customNames of a feature
addCustomNamesWithPrefix(String, FeatureList<?>) - Method in class org.anchoranalysis.feature.name.FeatureNameList
Add the customNames of a feature with a Prefix
AddDistanceTransform - Class in org.anchoranalysis.plugin.fiji.bean.define
Performs a Watershed on an EDT transform by bundling together several other beans
AddDistanceTransform() - Constructor for class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
 
addDoubleAsString(String, double) - Method in class org.anchoranalysis.overlay.OverlayProperties
 
AddDualTransformer - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
 
AddDualTransformer() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
 
addEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
Add an edge between two vertices.
addEdge(V, V, P) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
Add an edge between two vertices.
AddEdgeFilters - Class in org.anchoranalysis.plugin.imagej.bean.define
 
AddEdgeFilters() - Constructor for class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
 
addEdges(V, Collection<V>) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
Adds edge(s) from the vertex from to each element in toCollection.
addEnabledOutputFirst(String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
Adds enabled first-level outputs.
addEnabledOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
Adds enabled outputs from another OutputEnabledMutable.
addEnabledOutputSecond(String, String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
Adds enabled second-level outputs.
AddEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
 
AddEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.AddEnergy
 
addErrorDescription(StringBuilder) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
 
addErrorDescription(StringBuilder) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
addErrorDescription(StringBuilder) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
 
addErrorLevel(String) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
addErrorLevel(String, AnchorBean<?>) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
addFeatureListToStore(FeatureList<T>, String, boolean, NamedFeatureStore<T>) - Static method in class org.anchoranalysis.feature.list.FeatureListStoreUtilities
Adds a feature-list to the store
addFeatureListToStoreNoDuplicateDirectly(NamedProvider<FeatureList<FeatureInput>>, SharedFeatureMulti) - Static method in class org.anchoranalysis.feature.list.FeatureListStoreUtilities
 
addField(Field) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
 
addFormatted(String, Object...) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
 
addFormatted(String, Object...) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
addFormatted(String, Object...) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
 
addForSlice(int, int) - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
 
addForSlice(int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
 
addFrom(List<NamedBean<?>>) - Method in class org.anchoranalysis.bean.BeanInstanceMap
Populates from a list of NamedBean.
addFrom(BeanInstanceMap) - Method in class org.anchoranalysis.bean.BeanInstanceMap
Populates the entries from another BeanInstanceMap
addFrom(NamedProvider<Stack>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
 
addFromWithPrefix(NamedProvider<Stack>, String) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
 
addFromXmlFile(Path) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
Adds root-paths contained in a list of XML Beans in an xml file
addHistogram(Histogram) - Method in class org.anchoranalysis.math.histogram.Histogram
 
addIgnoreInfinity(double) - Method in class org.anchoranalysis.plot.AxisLimits
 
addIter(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
 
addIter(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
addIter(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
 
addLabelToDataset(DefaultCategoryDataset, T, int, String, String) - Method in class org.anchoranalysis.plot.index.BarPlot
 
addLabelToDataset(DefaultBoxAndWhiskerCategoryDataset, T, int, String, String) - Method in class org.anchoranalysis.plot.index.BoxPlot
 
addLabelToDataset(S, T, int, String, String) - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
 
addLeftObject(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
addLeftObjects(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
addListOfBeansToCollection(String, HierarchicalConfiguration, Collection<T>, Object) - Static method in class org.anchoranalysis.bean.xml.factory.HelperListUtilities
 
addManifestExperimentFileSet(Collection<File>, ManifestDeserializer, Logger) - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
 
addMultiple(RGBColor, int) - Method in class org.anchoranalysis.core.color.ColorList
 
addNewPath(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
Adds a new path with a point
addNoDuplicate(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
 
addObjectsNoBoundingBoxChange(Collection<T>) - Method in class org.anchoranalysis.spatial.box.BoundedList
Adds elements without changing the bounding-box
addObjectsToGraph(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
 
addObjectsWithColor(ObjectCollectionProvider, RGBColor) - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
Adds objects from a ObjectCollectionProvider all with one specific color
addOperationRecorder(WriteOperationRecorder) - Method in class org.anchoranalysis.io.output.outputter.Outputter
 
addOperationRecorder(WriteOperationRecorder) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
Adds an additional operation recorder alongside any existing recorders.
addPair(ObjectMask, ObjectMask, double) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
addPointsInMark(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
addPreserveName(List<NamedBean<S>>, NamedProviderStore<D>, CheckedFunction<S, D, OperationFailedException>) - Static method in class org.anchoranalysis.bean.store.BeanStoreAdder
Adds a list of named-items a container (using a bridge) using the same names in the destination container
addPreserveNameEmbedded(List<NamedBean<S>>, NamedProviderStore<D>, CheckedFunction<NamedBean<S>, D, OperationFailedException>) - Static method in class org.anchoranalysis.bean.store.BeanStoreAdder
Adds a list of named-items to a container (using a bridge) using the same names in the destination container
addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.Orientation
 
addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.Orientation
 
addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
addResultsFor(RowLabels, ResultsVector) - Method in class org.anchoranalysis.feature.io.results.group.GroupWriter
Adds a result to the group-writer, but doesn't write yet.
addResultsFor(RowLabels, ResultsVector) - Method in class org.anchoranalysis.feature.io.results.ResultsWriter
Adds feature-calculation results to be written.
addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in interface org.anchoranalysis.plugin.image.task.feature.ExportFeatureResultsAdder
Adds labeled results (which makes a row in a feature-table, and possibly other outputs).
addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
 
addRightObject(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
addRightObjects(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
addRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
Directly adds a row in the form of typed-values.
addRow(RowLabels, ResultsVector) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
Directly adds a row of feature-values.
addShift(ReadableTuple3i) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
Adds a shift to each point (modifying the existing points in memory), and returns them as a list
addSkippedAnnotationImage() - Method in interface org.anchoranalysis.plugin.annotation.comparison.AddAnnotation
 
addSkippedAnnotationImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
addSkippedAnnotationImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
 
addTo(Define) - Method in class org.anchoranalysis.bean.define.adder.Concatenate
 
addTo(Define) - Method in interface org.anchoranalysis.bean.define.adder.DefineAdder
 
addTo(Define) - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
 
addTo(Define) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
 
addTo(Define) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
 
addTo(Define) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
addTo(ObjectMask, int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic
Adds a constant-value to each voxel but only for voxels inside an object-mask
addTo(S, T) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
 
AddToAggregateItem<S,​T> - Interface in org.anchoranalysis.plugin.image.task.grouped
Adds an individual-item to an aggregate-item
AddToDefaults - Class in org.anchoranalysis.io.output.bean.rules
Adds additional outputs-names to be enabled to the defaults.
AddToDefaults() - Constructor for class org.anchoranalysis.io.output.bean.rules.AddToDefaults
 
addToErrorNode(ErrorNode) - Method in exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException
 
addToKeyValueParamsCollection(String, KeyValueParams) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
addToManager(MultiInputManager, String, String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManager
 
addToMarks(ColoredMarks) - Method in interface org.anchoranalysis.mpp.proposer.visualization.CreateProposalVisualization
 
addToMarks(ColoredMarks) - Method in class org.anchoranalysis.mpp.proposer.visualization.CreateProposeVisualizationList
 
addToRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.RowLabels
Adds the identifiers to a row to be outputted in a features CSV.
addToSharedObjects(MPPInitParams, ImageInitParams) - Method in interface org.anchoranalysis.mpp.io.input.InputForMPPBean
 
addToSharedObjects(MPPInitParams, ImageInitParams) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
addToSharedObjects(MPPInitParams, ImageInitParams) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
 
addToStackCollection(String, StackProvider) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
addToStackCollection(String, Stack) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
addToStore(NamedProviderStore<TimeSequence>) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
 
addToStore(NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
 
addToStore(NamedProviderStore<T>) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap
Copies all the existing entries into a NamedProvierStore
addToStore(NamedProviderStore<T>) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
 
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
addToStoreInferNames(NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
 
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
 
addToTypeValueCollection(Collection<TypedValue>, int) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
addToUpdatablePairList(ListUpdatableMarkSetCollection, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
addToVoxelList(int, int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
 
addUnannotatedImage() - Method in interface org.anchoranalysis.plugin.annotation.comparison.AddAnnotation
 
addUnannotatedImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
addUnannotatedImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
 
addUncoupledJobs(Collection<File>, ManifestDeserializer, Logger) - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
Adds job-manifests that don't have corresponding experiment-manifests.
addUnused(Histogram) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactoryHistogramReuse
 
addUnused(Histogram) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitonFactoryHistogram
 
addUnused(T) - Method in interface org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactory
 
addVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
Adds a vertex.
addVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
Adds a vertex.
addVisitedPoint(Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
Adds a visited-point to an existing path, or else makes a new one
addWeightedKernelFactories(List<WeightedKernel<T>>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
 
addWeightedKernelFactories(List<WeightedKernel<T>>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
addWeightedKernelFactories(List<WeightedKernel<T>>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
 
addWithIndex(RGBColor) - Method in class org.anchoranalysis.core.color.ColorList
 
addWithName(Define, String, AnchorBean<?>) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
 
addWithUnits(String, double, DoubleUnaryOperator, SpatialUnits.UnitSuffix) - Method in class org.anchoranalysis.overlay.OverlayProperties
 
AdjacentFile - Class in org.anchoranalysis.plugin.quick.bean.input
 
AdjacentFile() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
 
adjacentVerticesOutgoing(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
The vertices that are connected to a particular vertex by an outgoing edge
adjacentVerticesOutgoing(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
The vertices that are connected to a particular vertex by an outgoing edge
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
 
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
 
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
afterAllJobsAreExecuted(OutputSequenceIncrementing<Stack>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
afterAllJobsAreExecuted(ExperimentState, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
 
afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
 
afterAllJobsAreExecuted(SharedState<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
afterAllJobsAreExecuted(SharedStateExportFeatures<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
 
afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
 
afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
 
afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
 
afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
 
afterAllJobsAreExecuted(FromCSVSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
 
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class org.anchoranalysis.experiment.bean.task.Task
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
 
afterCopying(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
 
afterCopying(Path, boolean) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
 
afterCopying(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
 
afterCopying(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
 
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
 
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
 
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
 
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
 
afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
 
aggEnd(Aggregator) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiver
 
aggEnd(Aggregator) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
 
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
 
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
 
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
 
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
 
aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
 
AggIDCounter - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
 
AggIDCounter(int) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
AggregateAnnotations<S extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
Aggregates many per-image annotations together in form of a CSV file.
AggregateAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
 
AggregateReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
 
AggregateReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
 
AggregateReceiverList() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
 
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
 
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
 
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
 
aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
 
AggregateTriggerBank<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
 
AggregateTriggerBank(ExtractScoreSize<T>) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
 
Aggregator - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
 
Aggregator(int) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
AggregatorException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
 
AggregatorException() - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregatorException
 
AggregatorException(Exception) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregatorException
 
AggregatorException(String) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregatorException
 
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
 
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
 
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
 
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
 
aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
 
aggReport(Reporting<T>, Aggregator) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiver
 
aggReport(Reporting<T>, Aggregator) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
 
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
 
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
 
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
 
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
 
aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
 
aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiver
 
aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
 
All - Class in org.anchoranalysis.io.output.bean.enabled
All outputs are allowed irrespective of outputName.
All - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
Selects all possible channels from all possible stacks
All() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
 
ALL_DIMENSIONS - org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
The dilation applies in all dimensions (X, Y and Z)
allChannelsHaveIdenticalType() - Method in class org.anchoranalysis.image.core.stack.Stack
Determines if all channels have an identical voxel data-type.
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.Stack
Determines if all channels have a specific data-type.
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.TimeSequence
 
allFileTypes() - Method in class org.anchoranalysis.io.generator.ConcatenateFileTypes
 
allHeaders() - Method in class org.anchoranalysis.feature.io.results.LabelHeaders
The non-group and group headers combined (in this order respectively)
allLabels(NoSharedState) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
 
allLabels(ImageCSVLabellerInitParams) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
 
allLabels(ImageLabellerStringMapInitParams<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
 
allLabels(T) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
A set of identifiers for all groups that can be outputted by the labeller.
allMatchIntensity(ObjectMask, Voxels<T>, IntPredicate) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
Do all points on an object-mask match a predicate on the point's voxel-intensity?
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Allocates a new buffer of unsigned-bytes.
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Allocates a new (direct) buffer of unsigned-ints.
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Allocates a new (direct) buffer of unsigned-shorts.
allocateBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
 
allocateFloat(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
Allocates a new float voxel-buffers of given size.
allocateFloatArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
Creates an array of float voxel-buffers of given size.
allocateUnsignedByte(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
Allocates a new unsigned byte voxel-buffer of given size.
allocateUnsignedByteArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
Creates an array of unsigned byte voxel-buffers of given size.
allocateUnsignedInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
Allocates a new unsigned int voxel-buffers of given size.
allocateUnsignedIntArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
Creates an array of unsigned int voxel-buffers of given size.
allocateUnsignedShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
Allocates a new unsigned short voxel-buffers of given size.
allocateUnsignedShortArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
Creates an array of unsigned short voxel-buffers of given size.
AllowEmpty - Annotation Type in org.anchoranalysis.bean.annotation
Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
allSlices(Voxels<U>, Function<U, T>, Function<AbstractNativeImg<S, T>, S>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.Wrap
 
AllSlicesMaskEverythingNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
Only takes pixels where indexNonZero has a nonzero pixel
AllSlicesMaskEverythingNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
 
AllSlicesMaskNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
Gets all slices where indexNonZero has at least one non-zero pixel in that slice
AllSlicesMaskNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
 
allSuccessful() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
Did all jobs execute and completely successfully?
AllValuesOff - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
 
AllValuesOff() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOff
 
AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
Creates a new mask of particular dimensionality where all values are ON
AllValuesOn() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOn
 
Always - Class in org.anchoranalysis.plugin.image.bean.object.match
Specifies a single object that will always be the "match" for whatever source object.
Always() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Always
 
ALWAYS_NEW - org.anchoranalysis.image.core.channel.convert.ConversionPolicy
 
AlwaysAllowed - Class in org.anchoranalysis.io.output.writer
Allows every output, irrespective of whether the OutputterChecked allows the output-name.
AlwaysAllowed(OutputterChecked, Optional<WriterExecuteBeforeEveryOperation>) - Constructor for class org.anchoranalysis.io.output.writer.AlwaysAllowed
 
alwaysExecuteBeforeCallingLibrary() - Static method in class org.anchoranalysis.plugin.opencv.CVInit
This routine must always be executed at least once before calling any routines in the OpenCV library
AlwaysNew<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.replace
Always create a new session-input with no reuse or caching
AlwaysNew(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.AlwaysNew
Constructor with default means of creating a session-input
AlwaysNew(CacheCreator, FindChildStrategy) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.AlwaysNew
 
AnchorBean<F> - Class in org.anchoranalysis.bean
The base class of all beans used in Anchor.
AnchorBean() - Constructor for class org.anchoranalysis.bean.AnchorBean
 
AnchorBeanFactory - Class in org.anchoranalysis.bean.xml.factory
Base class for all Anchor-specific bean factories
AnchorBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.AnchorBeanFactory
 
AnchorCheckedException - Exception in org.anchoranalysis.core.exception
A base class for all checked exceptions used on the Anchor platform
AnchorCheckedException() - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
 
AnchorCheckedException(String) - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
 
AnchorCheckedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
 
AnchorCheckedException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
 
AnchorCombinableException - Exception in org.anchoranalysis.core.exception.combinable
An exception that can be combined with similar exceptions and summarized.
AnchorCombinableException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
 
AnchorDefaultBeanFactory - Class in org.anchoranalysis.bean.xml.factory
The default bean factory used for initializing AnchorBeans
AnchorDefaultBeanFactory(BeanInstanceMap) - Constructor for class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
 
AnchorFriendlyCheckedException - Exception in org.anchoranalysis.core.exception.friendly
A base class for particular checked-exceptions which are guaranteed to provide a user-friendly error description.
AnchorFriendlyCheckedException(String) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
A user-friendly error message WITHOUT a cause.
AnchorFriendlyCheckedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
A user-friendly error message and its cause.
AnchorFriendlyCheckedException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
A wrapped exception.
AnchorFriendlyRuntimeException - Exception in org.anchoranalysis.core.exception.friendly
A base class for particular runtime-exceptions which are guaranteed to provide a user-friendly error description.
AnchorFriendlyRuntimeException(String) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
A user-friendly error message WITHOUT a cause.
AnchorFriendlyRuntimeException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
A user-friendly error message and its cause.
AnchorFriendlyRuntimeException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
A wrapped exception.
AnchorImpossibleSituationException - Exception in org.anchoranalysis.core.exception.friendly
A run-time exception to throw in situations which should never occur, instead of
AnchorImpossibleSituationException() - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorImpossibleSituationException
 
AnchorNeverOccursException - Exception in org.anchoranalysis.core.exception
This is an exceotion that should never be thrown, but can be used for type-safety where an exception is needed
AnchorNeverOccursException() - Constructor for exception org.anchoranalysis.core.exception.AnchorNeverOccursException
 
AnchorRuntimeException - Exception in org.anchoranalysis.core.exception
A base class for all unchecked (runtime) exceptions used on the Anchor platform
AnchorRuntimeException() - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
 
AnchorRuntimeException(String) - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
 
AnchorRuntimeException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
 
AnchorRuntimeException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
 
And - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the result.
And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
Applies multiples filter with logical AND i.e.
And() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
 
And() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
 
AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
Combines two UpdatableBeforeConditions as LOGICAL ANDs
AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
 
AndKernel - Class in org.anchoranalysis.image.voxel.kernel
 
AndKernel(BinaryKernel, BinaryKernel) - Constructor for class org.anchoranalysis.image.voxel.kernel.AndKernel
 
AndList - Class in org.anchoranalysis.plugin.mpp.bean.check
 
AndList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.AndList
 
AndObjectsWithMasks - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask
Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
AndObjectsWithMasks() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
 
AngleRotation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
 
AngleRotation() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
 
AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider
Perona-Malik Anisotropic Diffusion
AnisotropicDiffusion() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
AnnealScheme - Class in org.anchoranalysis.mpp.bean.anneal
 
AnnealScheme() - Constructor for class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
 
Annotation - Interface in org.anchoranalysis.annotation
Base class for types of image annotations.
AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
 
AnnotationAggregateCSVGenerator() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator
 
AnnotationBackground - Class in org.anchoranalysis.annotation.io.bean
 
AnnotationBackground() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationBackground
 
AnnotationComparisonAssigner<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
 
AnnotationComparisonAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
 
AnnotationComparisonInput<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison
 
AnnotationComparisonInput(T, Tuple2<Comparer, Comparer>, Tuple2<String, String>, StackReader) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
AnnotationComparisonInputManager<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
 
AnnotationComparisonInputManager() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
AnnotationDeleter - Interface in org.anchoranalysis.annotation.io
 
annotationExistsCorrespondTo(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
 
AnnotationGroup<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
 
AnnotationGroup(String) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
AnnotationGroupList<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
 
AnnotationGroupList() - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
 
AnnotationGroupObject - Class in org.anchoranalysis.plugin.annotation.comparison
 
AnnotationGroupObject(String) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
 
AnnotationInputManager<T extends ProvidesStackInput,​S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean
 
AnnotationInputManager() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
 
AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label
 
AnnotationLabel() - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
 
annotationLabelFor(ProvidesStackInput) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
Returns a label describing the annotation, or empty() if this makes no sense
annotationLabelFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
annotationLabelFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
 
AnnotationMarksComparer<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparer
 
AnnotationMarksComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
 
annotationPathFor(ProvidesStackInput) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
 
annotationPathFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
 
AnnotationReader<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
 
AnnotationWithMarks - Interface in org.anchoranalysis.annotation.mark
An image-annotation that involves a mark-collection.
AnnotationWithStrategy<T extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io
An annotation that has been combined with its strategy.
AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class org.anchoranalysis.annotation.io.AnnotationWithStrategy
 
AnnotationWriter<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
 
AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean
 
AnnotatorStrategy() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
 
Anonymize - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
Copies files to a number 001 002 etc.
Anonymize() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
 
any() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
Returns voxels that are not cast to any specific buffer type
anyDimensionIsLargerThan(Extent) - Method in class org.anchoranalysis.spatial.Extent
Returns true if any dimension in this extent is larger than the corresponding dimension in other extent
anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
 
anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
 
anyExists() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
Does at least one value satisfy the predicate - across all voxels?
anyMatch(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Does the predicate evaluate to true on any object in the collection?
anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Tries to apply a predicate to all the remaining buffer locations, returning true if the predicate matches.
AnySliceCenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
The center ps of at least one slice should be on the stack Tries overall center point first, and then projects it onto each slice
AnySliceCenterOnMask() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.AnySliceCenterOnMask
 
append(Optional<FeatureList<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
Appends one or more additional (optional) feature-lists
AppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
A CSV that is appended from the root of a project
AppendCsv() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
 
AppendFilePath - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
 
AppendFilePath() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendFilePath
 
AppendHistogram - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
 
AppendHistogram() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
 
AppendKeyValueParams - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
 
AppendKeyValueParams() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
 
AppendMarks - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
 
AppendMarks() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendMarks
 
AppendObjects - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
 
AppendObjects() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendObjects
 
AppendStack - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
A stack from a stack-collection
AppendStack() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
 
AppendStackDirect - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
A stack from a stack-collection
AppendStackDirect() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
 
apply(int) - Method in interface org.anchoranalysis.core.functional.checked.CheckedIntFunction
Calls the function
apply(int, int) - Method in interface org.anchoranalysis.core.functional.checked.IntBinaryOperation
 
apply(Integer) - Method in class org.anchoranalysis.core.index.IndexBridge
 
apply(String, Path) - Static method in class org.anchoranalysis.io.generator.text.WriteStringToFile
 
apply(Throwable, Writer, String, int, boolean) - Static method in class org.anchoranalysis.core.exception.friendly.RecursivelyDescribeExceptionStack
Incrementally adds a line to a string builder with the message of each exception moving onto the next nested exception until there are no more
apply(IFormatReader, ReadOptions, int) - Method in class org.anchoranalysis.io.bioformats.DimensionsCreator
 
apply(ImageInitParams) - Static method in class org.anchoranalysis.image.bean.nonbean.init.CreateCombinedStack
 
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskAnd
Performs a AND operation on each voxel in two masks, writing the result onto the second mask.
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskIfHighLow
Performs a iff first==HIGH and second==LOW then LOW operation on each voxel in two masks, writing the result onto the second mask.
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskOr
Performs a OR operation on each voxel in two masks, writing the result onto the first mask.
apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskXor
Performs a XOR (exclusive OR) operation on each voxel in two masks, writing the result onto the first mask.
apply(BinaryKernel, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
 
apply(BinaryKernel, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
 
apply(ObjectMask, double, int, int) - Static method in class org.anchoranalysis.plugin.points.bean.contour.SplitContourSmoothingSpline
1.
apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskAnd
Performs a AND operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskXor
Performs a XOR (exclusive OR) operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
apply(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedFunction
Calls the function
apply(S, T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedBiFunction
Calls the function
apply(T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedUnaryOperator
 
applyAsDouble(T, U) - Method in interface org.anchoranalysis.core.functional.checked.CheckedToDoubleBiFunction
Applies this function to the given arguments.
applyAsInt(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedToIntFunction
Calls the function
applyCoefficientsToMark(DoubleMatrix2D, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
 
applyDelta(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
Applies the changes to enable or disable additional outputs, if they are defined.
applyFitResultToMark(Ellipsoid, Dimensions, double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
applyForCount(BinaryKernel, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
 
applyForCount(CountKernel, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
Applies the kernel to voxels and sums the returned value
applyForCount(CountKernel, Voxels<UnsignedByteBuffer>, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
Applies the kernel to voxels and sums the returned value
applyForCountOnMask(BinaryKernel, Voxels<UnsignedByteBuffer>, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
 
applyGlobal(List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.OutlineTraverser
Root point is arbitrarily chosen from object
applyGlobal(Point3i, List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.OutlineTraverser
 
ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask
Applies an ImageJ (2D) morphological operation to voxels
applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class org.anchoranalysis.bean.initializable.property.PropertyInitializer
Applies the initialization to a property using the current or extracted params if possible.
ApplyKernel - Class in org.anchoranalysis.image.voxel.kernel
Applies a kernel to a Voxel Box
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
 
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
 
applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
 
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
 
applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
 
applyOperation(Dimensions, UnaryOperator<Stack>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
Applies an operation on each stack in the collection and returns a new derived collection
applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation
 
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
 
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
 
applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
 
ApplyPermutations<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.permute
Applies a PermuteProperty to a bean to create new duplicated beans each with a permutation
ApplyPermutations(ApplyPermutations.NameGetter<T>, ApplyPermutations.NameSetter<T>) - Constructor for class org.anchoranalysis.bean.permute.ApplyPermutations
 
ApplyPermutations.NameGetter<S> - Interface in org.anchoranalysis.bean.permute
 
ApplyPermutations.NameSetter<S> - Interface in org.anchoranalysis.bean.permute
 
applyPermutationsToCreateDuplicates(List<T>, PermuteProperty<S>, PermutationSetter) - Method in class org.anchoranalysis.bean.permute.ApplyPermutations
Takes a list of beans, and creates a permuted version, updating the custom names
applyRadiiSubtractScale(double, double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
applyRankFilter(Channel, int, int) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper
Applies a 2D rank-filter to each slice independently.
ApplyRegExSubstitution - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
A regular expression substitution (replaceAll) is applied to the relative-path
ApplyRegExSubstitution() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
 
applyStrategy(MergeCandidate) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeStrategy
 
applyUntilPositive(CountKernel, Voxels<UnsignedByteBuffer>, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
Applies the kernel to voxels until a positive value is returned, then exits with true
ArbitraryInsidePoint - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
Calculates deterministicly a point that is definitely inside the object-mask.
ArbitraryInsidePoint() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
 
ArbitraryInsidePoint(String) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
 
ArbitraryPointCommon - Class in org.anchoranalysis.mpp.feature.addcriteria
If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
ArbitraryPointCommon() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
 
Area<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
Area of the stack (XY dimensions only, Z dimension is not considered)
Area() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
 
areAllPointsInBigNeighborhood(List<Point3i>) - Static method in class org.anchoranalysis.image.core.points.PointsNeighborChecker
Are all points in a list neighboring the next point in the list?
AreaPhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
Area expressed in physical coordinates
AreaPhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
 
AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
Area expressed as square pixels
AreaPixels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
 
AreaPixels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
 
areEqual(double, double) - Static method in class org.anchoranalysis.math.arithmetic.DoubleUtilities
Are the two numbers equal?
areEqual(float, float) - Static method in class org.anchoranalysis.math.arithmetic.FloatUtilities
Are the two numbers equal?
areNeighborsDistinct(List<Point3i>) - Static method in class org.anchoranalysis.image.core.points.PointsNeighborChecker
Makes sure no successive neighbors are equal
arePointsNeighbors(Point3i, Point3i) - Static method in class org.anchoranalysis.image.core.points.PointsNeighborChecker
 
areXmlEqual(Document, Document) - Static method in class org.anchoranalysis.test.TestLoader
Does a check if the XML documents are equal
ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path
Converts string passed as arguments.
arithmetic() - Method in class org.anchoranalysis.image.core.channel.Channel
 
arithmetic() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
 
arithmetic() - Method in class org.anchoranalysis.image.voxel.Voxels
Methods to manipulate the voxel-values via arithmetic
arithmetic() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
ArithmeticWithConstantBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.
ArithmeticWithConstantBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
 
ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
ArithmeticWithConstantConditionallyWriteBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
 
ArrangeRaster - Class in org.anchoranalysis.image.bean.provider.stack
Creates a stack that tiles (or otherwise combines) other providers
ArrangeRaster() - Constructor for class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
 
ArrangeStack - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
 
ArrangeStackBean - Class in org.anchoranalysis.image.bean.spatial.arrange
 
ArrangeStackBean() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.ArrangeStackBean
 
ArrangeStackException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
 
ArrangeStackException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException
 
ArrangeStackException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException
 
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
The array of the buffer ala ByteBuffer.array().
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
The array of the buffer ala ShortBuffer.array().
asByte() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
asByte(ImageProcessor) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToVoxelBuffer
Convert a ImageProcessor to VoxelBuffer<UnsignedByteBuffer>
asByteOrCreateEmpty(boolean) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
Reuses the existing buffer if byte, otherwise creates a new empty byte buffer
AsCollection - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
 
AsCollection() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsCollection
 
asCollectionOrderNotPreserved() - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements
Returns the scaled-elements as a collection but without preserving the original element order.
asExtent() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
Creates an extent with identical width and height and depth (z-extent) of 1
asExtent(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
Creates an extent with identical width and height and a specific depth (z-extent)
asFloat() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
asInt() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
asList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
asList() - Method in class org.anchoranalysis.feature.name.FeatureNameList
 
asList() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
Exposes the underlying objects as a list
asList() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
asList() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
 
asListChannels() - Method in class org.anchoranalysis.image.core.stack.Stack
 
asListOrderPreserved(List<T>) - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements
Returns a list of scaled-elements corresponding to a list of unscaled-elements
asMap() - Method in class org.anchoranalysis.core.identifier.name.MapCreate
 
AsMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
AsMark() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
 
asMarks() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
AsObject - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
AsObject() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
 
AsObjectMask - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask feature
AsObjectMask() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
 
asObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
 
asOperationFailedException() - Method in exception org.anchoranalysis.core.index.GetOperationFailedException
 
asOrderedArray() - Method in class org.anchoranalysis.spatial.Extent
 
asPath() - Method in class org.anchoranalysis.bean.shared.path.RootPath
 
asPoint() - Method in class org.anchoranalysis.image.bean.spatial.Padding
 
assertCalc(ResultsVector, Object...) - Static method in class org.anchoranalysis.test.feature.plugins.ResultsVectorTestUtilities
 
assertDoubleResult(String, Feature<T>, T, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
 
assertDoubleResult(String, Feature<T>, T, Optional<SharedObjects>, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
 
assertDoubleResult(String, Feature<T>, T, T, double, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculatorDuo
 
assertIntResult(String, Feature<T>, T, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
 
assertIntResult(String, Feature<T>, T, Optional<SharedObjects>, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
 
assertIntResult(String, Feature<T>, T, T, int, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculatorDuo
 
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
assertValid() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
asShort() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
asShort(ImageProcessor) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToVoxelBuffer
Convert a ImageProcessor to VoxelBuffer<UnsignedShortBuffer>
assignAccepted(DualMarks) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
Assigns marks with an overall accepted state.
assignBestFromCurrent() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
 
assignBoundingBox(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundedList
Assigns a new containing bounding-box.
assignBoundingBoxAndMap(BoundingBox, UnaryOperator<T>) - Method in class org.anchoranalysis.spatial.box.BoundedList
Assigns a new containing bounding-box and maps each individual element.
assignCurrent(Optional<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
 
assignDescription(ManifestDirectoryDescription) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
Assigns a description, which may not already exist.
assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Assigns a value to any voxel whose intensity matches a predicate, reading and writing the buffer as an int.
assignFrom(CachedSupplierBase<T>) - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
 
assignFrom(Mark) - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
Assigns a new mark to replace the existing mark.
AssignFromChannel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
Copies the pixels from channelAssignFrom to channel (possibly masking)
AssignFromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
 
AssignFromIntersectingObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
Matches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target object
AssignFromIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
 
AssignFromParams - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
 
AssignFromParams() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
 
assignFunction(String) - Method in class org.anchoranalysis.io.manifest.ManifestDescription
Assigns a new function.
assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
 
assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
If the sequence-type supports a different maximum-index to that derived from the elements SequenceType.update(T), this assigns it.
assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
 
Assignment - Interface in org.anchoranalysis.annotation.io.assignment
 
AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator
Outputs a raster showing an Assignment on a background.
AssignmentGenerator(DisplayStack, IntFunction<ColorPool>, boolean, Tuple2<String, String>, boolean, int) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
 
AssignmentMaskIntersection - Class in org.anchoranalysis.annotation.io.assignment
Calculates statistics (DICE, Jaccard etc.) based upon corresponding two object-masks
AssignmentMaskIntersection(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
 
AssignmentObjectFactory - Class in org.anchoranalysis.annotation.io.assignment
 
AssignmentObjectFactory(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignmentObjectFactory
 
AssignmentOverlapFromPairs - Class in org.anchoranalysis.annotation.io.assignment
Pairs objects in left with objects in right
AssignmentOverlapFromPairs() - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
AssignMode<S,​T,​U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
How assignments and other decisions are made in the SimulatedAnnealing optimizaton
AssignMode() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
 
assignOff() - Method in class org.anchoranalysis.image.core.mask.Mask
 
assignOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
assignOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Assigns OFF value to voxels, expecting global coordinates
assignOn() - Method in class org.anchoranalysis.image.core.mask.Mask
 
assignOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
assignOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Assigns ON value to voxels, expecting global coordinates
assignParentFolder(Optional<MutableDirectory>) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
assignPath(Path) - Method in class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
 
assignPaused(DualMarks) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
Assigns marks with an overall paused state.
assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
Assigns a priority to a potential merge
AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority
 
AssignPriority() - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
 
AssignPriorityFromImprovement - Class in org.anchoranalysis.plugin.image.object.merge.priority
Allows merges if there is an increase in the payload i.e.
AssignPriorityFromImprovement(PayloadCalculator) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
 
AssignPriorityFromPair - Class in org.anchoranalysis.plugin.image.object.merge.priority
Calculates pair-feature on each potential merge, and this value determines priority..
AssignPriorityFromPair(FeatureCalculatorSingle<FeatureInputPairObjects>, double, RelationToValue) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
 
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
 
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
 
assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
 
assignProposal(Optional<T>, KernelWithIdentifier<S>) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
assignProposal(OptimizationStep<S, T>, TransformationContext, KernelWithIdentifier<S>) - Method in interface org.anchoranalysis.mpp.segment.kernel.KernelAssigner
 
assignProposal(OptimizationStep<S, T>, TransformationContext, KernelWithIdentifier<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerAddErrorLevel
 
assignProposal(OptimizationStep<S, T>, TransformationContext, KernelWithIdentifier<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerCalculateEnergyFromKernel
 
assignRejected(DualMarks, T) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
Assigns marks with an overall rejected state.
assignType(String) - Method in class org.anchoranalysis.io.manifest.ManifestDescription
Assigns a new type.
assignValue(int) - Method in class org.anchoranalysis.image.core.channel.Channel
 
assignValue(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes etc.
assignValue(int) - Method in class org.anchoranalysis.image.voxel.Voxels
Provides a means to assign a constant-value to some or all of the voxels
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsAsFloat
 
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsAsInt
 
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsAsShort
 
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
 
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
AssignValue - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
Assigns a constant (scalar) value to the portion of the image covered by a mask
AssignValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
 
AsSingle - Class in org.anchoranalysis.mpp.feature.bean.energy.element
Extracts one of the memos from the pair, and processes as a FeatureSingleMemo
AsSingle() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
 
AsSingleMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
 
AsSingleMark() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsSingleMark
 
associatedFile() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
 
associateXml(XMLConfiguration) - Method in interface org.anchoranalysis.bean.xml.AssociateXmlUponLoad
Associated
associateXml(XMLConfiguration) - Method in class org.anchoranalysis.experiment.bean.Experiment
 
associateXml(XMLConfiguration) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
AssociateXmlUponLoad - Interface in org.anchoranalysis.bean.xml
For classes that wish to have a XmlConfiguration associated with them
asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStack
 
asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
 
asStack() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
asTuple() - Method in class org.anchoranalysis.spatial.Extent
Exposes the extent as a tuple.
asVoxels() - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
The target buffer
atanHandlingNan(double) - Static method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
atBorder(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
AtBorderBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
 
AtBorderBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
 
atBorderXY(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
 
AtBorderXY() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
 
atBorderZ(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
 
AtBorderZ() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ
 
atCorner(ReadableTuple3i, VoxelsExtracter<T>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
Projects a VoxelsExtracter to a corner in a larger global space
AtIndex - Class in org.anchoranalysis.plugin.image.bean.object.provider
Creates a new object-collection with only a single element (at a particular index) in the existing collection.
AtIndex() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
 
AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.groupfiles.check
 
AtLeastZSlices() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
 
AtScale - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
Perform a segmentation at a different scale, and then fit the results back to the original scale.
AtScale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
 
attachObject(Channel) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
 
attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
 
attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
 
attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
 
attachObject(S) - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached
 
AutoLocalThreshold - Class in org.anchoranalysis.plugin.fiji.bean.mask.provider
Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
AutoLocalThreshold() - Constructor for class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
 
Autoname - Class in org.anchoranalysis.plugin.io.bean.channel.map
Names of the channels from the metadata if it exists, or after RGB, or by index
Autoname() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.Autoname
 
AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction
 
AxisAlignedUnitVector() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
 
AxisLimits - Class in org.anchoranalysis.plot
 
AxisLimits() - Constructor for class org.anchoranalysis.plot.AxisLimits
 
AxisLimits(double, double) - Constructor for class org.anchoranalysis.plot.AxisLimits
 
AxisRatioEllipsoid - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
 
AxisRatioEllipsoid() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.AxisRatioEllipsoid
 
AxisType - Enum in org.anchoranalysis.spatial.axis
 
AxisTypeConverter - Class in org.anchoranalysis.spatial.axis
Converts to/from AxisType to string representations and integer index (0 for X, 1 for Y, 2 for Z)
AxisTypeException - Exception in org.anchoranalysis.spatial.axis
 
AxisTypeException(String) - Constructor for exception org.anchoranalysis.spatial.axis.AxisTypeException
 

B

background() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
background(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksFlattenedGenerator
 
background(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGenerator
 
background(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
 
BackgroundCreator - Class in org.anchoranalysis.mpp.io.output
 
backgroundStack() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
BackgroundSubtractor - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider
 
BackgroundSubtractor() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
 
BarPlot<T> - Class in org.anchoranalysis.plot.index
A bar plot, stacked or non-stacked.
BarPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, Double>, GetForSeries<T, Paint>, boolean) - Constructor for class org.anchoranalysis.plot.index.BarPlot
 
Base<T> - Class in org.anchoranalysis.image.voxel.extracter
 
Base(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.extracter.Base
 
BASE - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
 
BBoxRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
BBoxRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.BBoxRatio
 
BeanDuplicateException - Exception in org.anchoranalysis.bean.error
An exception occurs when the duplication of a bean fails
BeanDuplicateException(Exception) - Constructor for exception org.anchoranalysis.bean.error.BeanDuplicateException
 
BeanDuplicateException(String) - Constructor for exception org.anchoranalysis.bean.error.BeanDuplicateException
 
BeanDuplicateException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.error.BeanDuplicateException
 
BeanField - Annotation Type in org.anchoranalysis.bean.annotation
Indicates that a field in an Anchor Bean class is to be treated as a bean-field.
beanFor(Field, AnchorBean<?>) - Static method in class org.anchoranalysis.bean.permute.setter.PermutationSetterUtilities
Finds a bean corresponding to a field (exceptionally handling a List by taking the first item in it)
BeanInitParams - Interface in org.anchoranalysis.bean.initializable.params
Parent class for all parameters used to initialise beans in InitializableBean
BeanInstanceMap - Class in org.anchoranalysis.bean
Maps a AnchorBean family-type to some beans belong to the family.
BeanInstanceMap() - Constructor for class org.anchoranalysis.bean.BeanInstanceMap
 
BeanMisconfiguredException - Exception in org.anchoranalysis.bean.error
If a Bean is misconfigured
BeanMisconfiguredException(String) - Constructor for exception org.anchoranalysis.bean.error.BeanMisconfiguredException
 
BeanMisconfiguredException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.error.BeanMisconfiguredException
 
BeanMisconfiguredXmlException - Exception in org.anchoranalysis.bean.xml.error
A bean's XML is thrown when a bean has misconfigured XML
BeanMisconfiguredXmlException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
Constructor
BeanMisconfiguredXmlException(Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
Constructor
BeanPathUtilities - Class in org.anchoranalysis.bean.xml.factory
 
BeanProviderAsStackBase<T,​S> - Class in org.anchoranalysis.image.bean.provider
A provider base-class that as well as providing type S, also provide a stack
BeanProviderAsStackBase() - Constructor for class org.anchoranalysis.image.bean.provider.BeanProviderAsStackBase
 
BeanStoreAdder - Class in org.anchoranalysis.bean.store
 
BeanStrangeException - Exception in org.anchoranalysis.bean.error
When something quite strange happens that we don't usually want to catch.
BeanStrangeException(String) - Constructor for exception org.anchoranalysis.bean.error.BeanStrangeException
 
BeanStrangeException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.error.BeanStrangeException
 
BeanTestChecker - Class in org.anchoranalysis.test.experiment
Checks to see if a bean has been misconfigured, when created manually in tests (thereby skipping the usual checks during the BeanXML loading process).
BeanXmlException - Exception in org.anchoranalysis.bean.xml.error
An exception that occurs when one cannot process BeanXML for some reason
BeanXmlException(String) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanXmlException
 
BeanXmlException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanXmlException
 
BeanXmlException(Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanXmlException
 
BeanXmlLoader - Class in org.anchoranalysis.bean.xml
Creates beans based on XML specifying their properties (including nested children).
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.task.Task
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
 
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
 
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.feature.bean.Feature
Dummy method, that children can optionally override
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
 
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
 
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
 
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
 
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
 
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
 
beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
 
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
 
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
 
beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
 
beforeCalcWithImageInitParams(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
 
beforeCalcWithImageInitParams(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
 
beforeCalcWithImageInitParams(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
 
BeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
 
beforeCopying(Path, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
 
beforeCopying(Path, int) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
 
beforeCopying(Path, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
 
beforeCopying(Path, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
 
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
 
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
 
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
 
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
 
beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
 
BidirectionalBound - Class in org.anchoranalysis.mpp.bound
 
BidirectionalBound(Optional<ResolvedBound>, Optional<ResolvedBound>) - Constructor for class org.anchoranalysis.mpp.bound.BidirectionalBound
 
BinaryClassifierImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
 
BinaryClassifierImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
 
BinaryKernel - Class in org.anchoranalysis.image.voxel.kernel
 
BinaryKernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.BinaryKernel
 
BinaryKernelMorph3 - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
 
BinaryKernelMorph3(BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
 
BinaryKernelMorph3Extent - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
 
BinaryKernelMorph3Extent(BinaryValuesByte, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
 
BinaryNotOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation
Selects anything that is not off voxels from a binary mask.
BinaryNotOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
 
BinaryNotOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation
Selects anything that is not on voxels from a binary mask.
BinaryNotOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
 
BinaryOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation
Selects only the off voxels from a binary mask.
BinaryOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
 
BinaryOnOffSetter - Interface in org.anchoranalysis.image.voxel.binary
 
BinaryOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation
Selects only the on pixels from a binary mask.
BinaryOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
 
binaryOperation(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, IntBinaryOperation) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Iterate over each voxel in a bounding-box - applying a binary operation with values from two input Voxels<UnsignedByteBuffer> for each slice and writing it into an output Voxels<UnsignedByteBuffer>.
BinaryOutcomeImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
 
BinaryOutcomeImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
 
binaryResizing(int) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
 
BinarySegmentation - Class in org.anchoranalysis.image.bean.segment.binary
 
BinarySegmentation() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation
 
BinarySegmentationOne - Class in org.anchoranalysis.image.bean.segment.binary
 
BinarySegmentationOne() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
 
BinarySegmentationParameters - Class in org.anchoranalysis.image.bean.nonbean.segment
Parameters that are optionally associated with a BinarySegmentation
BinarySegmentationParameters() - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
 
BinarySegmentationParameters(Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
 
BinarySegmentationParameters(Optional<Histogram>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
 
BinarySegmentationParameters(Resolution, Optional<Histogram>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
Constructor
BinarySegmentationReference - Class in org.anchoranalysis.image.bean.segment.binary
 
BinarySegmentationReference() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
 
binarySegmentations() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
BinarySegmentationThreshold - Class in org.anchoranalysis.image.bean.segment.binary
 
BinarySegmentationThreshold() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
 
BinarySegmentByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
Performs a binary-segmentation using the upstream objects as masks.
BinarySegmentByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
 
binaryValues() - Method in class org.anchoranalysis.image.core.mask.Mask
 
binaryValues() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
Which two intensity values represent OFF and ON states
binaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
BinaryValues - Class in org.anchoranalysis.image.voxel.binary.values
Two values representing int binary states in an unsigned-byte buffer e.g.
BinaryValues(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValues
 
binaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
BinaryValuesByte - Class in org.anchoranalysis.image.voxel.binary.values
Two values representing byte binary states in an unsigned-byte buffer e.g.
BinaryValuesByte(byte, byte) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
 
BinaryValuesByte(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
 
binaryVoxels() - Method in class org.anchoranalysis.image.core.mask.Mask
 
binaryVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
BinaryVoxels<T> - Class in org.anchoranalysis.image.voxel.binary
Like Voxels but should only contain two distinct intensity-values representing ON and OFF states.
BinaryVoxels(Voxels<T>, BinaryValues) - Constructor for class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
BinaryVoxelsBase - Class in org.anchoranalysis.image.bean.threshold.relation
 
BinaryVoxelsBase() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
 
BinaryVoxelsFactory - Class in org.anchoranalysis.image.voxel.binary
 
binaryVoxelsFor(Voxels<T>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
bind(FeatureList<T>, FeatureInitParams, SharedFeatureMulti, Logger) - Method in class org.anchoranalysis.feature.session.strategy.replace.bind.BoundReplaceStrategy
 
BindFailedException - Exception in org.anchoranalysis.io.output.outputter
 
BindFailedException(String) - Constructor for exception org.anchoranalysis.io.output.outputter.BindFailedException
 
BindFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.output.outputter.BindFailedException
 
BioformatsOpenedRaster - Class in org.anchoranalysis.io.bioformats
 
BioformatsOpenedRaster(IFormatReader, IMetadata, ReadOptions) - Constructor for class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
 
BioformatsReader - Class in org.anchoranalysis.io.bioformats.bean
 
BioformatsReader() - Constructor for class org.anchoranalysis.io.bioformats.bean.BioformatsReader
 
BioformatsReader(ReadOptions) - Constructor for class org.anchoranalysis.io.bioformats.bean.BioformatsReader
 
BioformatsWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
Base class for writing a stack to the filesystem using the Bioformats library.
BioformatsWriter() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
 
bitDepth() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
 
bitDepth() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
BitDepth - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
 
BitDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
 
BlackBackgroud - Class in org.anchoranalysis.plot.bean.colorscheme
A black background and white axes.
BlackBackgroud() - Constructor for class org.anchoranalysis.plot.bean.colorscheme.BlackBackgroud
 
blockUntilLoaded() - Static method in class org.anchoranalysis.plugin.opencv.CVInit
Blocks a thread until the initialization has completed.
blue() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
 
blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
 
blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
 
Blur - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
Blur() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
 
BlurGaussian3D - Class in org.anchoranalysis.plugin.image.bean.blur
Performs a Gaussian Blur in 3D
BlurGaussian3D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
 
BlurGaussianEachSlice2D - Class in org.anchoranalysis.plugin.image.bean.blur
Performs a Gaussian-blur in 2D on each slice independently
BlurGaussianEachSlice2D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
 
BlurStrategy - Class in org.anchoranalysis.plugin.image.bean.blur
A method for applying blurring to an image
BlurStrategy() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
 
bothNameAndParams() - Static method in class org.anchoranalysis.feature.list.NamedFeatureStoreFactory
 
Bound - Class in org.anchoranalysis.mpp.bean.bound
 
Bound() - Constructor for class org.anchoranalysis.mpp.bean.bound.Bound
 
boundaryMax(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
 
boundaryMax(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
Boundary to define the maximum accepted value in the range
boundaryMax(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
 
boundaryMin(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
 
boundaryMin(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
Boundary to define the minimum accepted value in the range
boundaryMin(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
 
BoundCalculator - Class in org.anchoranalysis.mpp.bean.bound
 
BoundCalculator() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundCalculator
 
BoundCalculatorException - Exception in org.anchoranalysis.mpp.bound
 
BoundCalculatorException(Exception) - Constructor for exception org.anchoranalysis.mpp.bound.BoundCalculatorException
 
BoundCalculatorException(String) - Constructor for exception org.anchoranalysis.mpp.bound.BoundCalculatorException
 
boundChanged(BoundChangeEvent) - Method in interface org.anchoranalysis.core.index.bounded.BoundChangeListener
 
BoundChangeEvent - Class in org.anchoranalysis.core.index.bounded
 
BoundChangeEvent(Object, BoundChangeEvent.BoundType) - Constructor for class org.anchoranalysis.core.index.bounded.BoundChangeEvent
 
BoundChangeEvent.BoundType - Enum in org.anchoranalysis.core.index.bounded
 
BoundChangeListener - Interface in org.anchoranalysis.core.index.bounded
 
BoundDegrees - Class in org.anchoranalysis.mpp.bean.bound
 
BoundDegrees() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees
 
BoundDegrees(BoundDegrees) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees
 
BoundedIndexContainer<T> - Interface in org.anchoranalysis.core.index.bounded
 
BoundedIndexContainerBridge<H,​S,​E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge
Bridges calls from hidden-type to external-type.
BoundedIndexContainerBridge(BoundedIndexContainer<H>) - Constructor for class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
 
BoundedIndexContainerBridgeWithIndex<H,​S,​E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge
Bridges calls from hidden-type to external-type.
BoundedIndexContainerBridgeWithIndex(BoundedIndexContainer<H>, BridgeElementWithIndex<H, S, E>) - Constructor for class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithIndex
 
BoundedIndexContainerBridgeWithoutIndex<H,​S,​E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge
Bridges calls from hidden-type to external-type.
BoundedIndexContainerBridgeWithoutIndex(BoundedIndexContainer<H>, CheckedFunction<H, S, E>) - Constructor for class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithoutIndex
 
BoundedIndexContainerFromList<T> - Class in org.anchoranalysis.core.index.bounded
 
BoundedIndexContainerFromList(List<T>) - Constructor for class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
 
BoundedList<T> - Class in org.anchoranalysis.spatial.box
One or more elements, each with an individual bounding-box, and collectively with a bounding-box that fully contains them all.
BoundedRange - Interface in org.anchoranalysis.core.index.bounded
 
BoundedRangeIncomplete - Interface in org.anchoranalysis.core.index.bounded
A range of discrete integers that is not complete (missing many integers).
BoundedRangeIncompleteDynamic - Interface in org.anchoranalysis.core.index.bounded
 
boundedVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
BoundedVoxels<T> - Class in org.anchoranalysis.image.voxel
Voxel-data that is bounded to exist in a particular bounding-box in an image.
BoundedVoxels(BoundedVoxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels
Copy constructor
BoundedVoxels(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels
Creates voxels bounded to match the entire voxel-data at the origin.
BoundedVoxels(BoundingBox, Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels
Creates voxels with a corresponding bounding box.
BoundedVoxelsFactory - Class in org.anchoranalysis.image.voxel
 
boundingBox() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
boundingBox() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
A bounding-box that associates voxels to a particular part of an image
boundingBox() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
boundingBox() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
A bounding-box enclosing the voxelized representation of the mark
boundingBox() - Method in class org.anchoranalysis.spatial.box.BoundedList
A bounding-box that must contain all elements in the collection
BoundingBox - Class in org.anchoranalysis.spatial.box
A bounding-box in 2 or 3 dimensions.
BoundingBox(Extent) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox
Constructs a bounding-box to cover the entirety of a certain extent.
BoundingBox(Point3d, Point3d) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox
Creates from two double points (a minimum corner and a maximum corner).
BoundingBox(ReadableTuple3i, Extent) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox
 
BoundingBox(ReadableTuple3i, ReadableTuple3i) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox
Creates from two int points (a minimum corner and a maximum corner).
BoundingBoxAlongAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
 
BoundingBoxAlongAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
 
BoundingBoxCalculator - Class in org.anchoranalysis.mpp.mark.conic
Functions to calculate a bounding-box for a point surrounded by some form of radii
BoundingBoxContains - Class in org.anchoranalysis.spatial.box
Does a bounding box contain other objects? e.g.
BoundingBoxContains(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxContains
 
BoundingBoxDistance - Class in org.anchoranalysis.spatial.box
Calculates distance between two bounding boxes
BoundingBoxesOnPlane - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
Describes a set of bounding boxes on top of a plane
BoundingBoxesOnPlane(Extent) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
BoundingBoxesOnPlane(Extent, BoundingBox) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
BoundingBoxExtent - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
 
BoundingBoxExtent() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
 
BoundingBoxExtentAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
 
BoundingBoxExtentAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
 
boundingBoxFlattened() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
The bounding-box flattened in z dimension
boundingBoxFor(T) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
A bounding-box for a given element.
boundingBoxForRegion(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
BoundingBoxFromPoints - Class in org.anchoranalysis.image.core.points
Creates a bounding-box from one or more points
BoundingBoxIntersection - Class in org.anchoranalysis.mpp.feature.addcriteria
 
BoundingBoxIntersection - Class in org.anchoranalysis.spatial.box
Methods for checking intersection between a particular bounding-box and others
BoundingBoxIntersection() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
 
BoundingBoxIntersection(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxIntersection
 
BoundingBoxMaximumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
 
BoundingBoxMaximumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
 
BoundingBoxMerger - Class in org.anchoranalysis.spatial.box
 
BoundingBoxMinimumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
 
BoundingBoxMinimumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
 
BoundingBoxNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
 
BoundingBoxNumberVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
 
boundingBoxThatSpansInput(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
 
boundingBoxThatSpansInput(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
 
boundingBoxThatSpansInput(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects)
BoundingBoxUnion - Class in org.anchoranalysis.spatial.box
Performs union of a bounding-box with other entities
BoundingBoxUnion(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxUnion
 
BoundingBoxZDistance - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
Measures the amount of distance in Z for the bounding box.
BoundingBoxZDistance() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZDistance
 
BoundingBoxZOverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
Measures the amount of bounding box overlap in the Z dimension
BoundingBoxZOverlapRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
 
BoundMinMax - Class in org.anchoranalysis.mpp.bean.bound
 
BoundMinMax() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
BoundMinMax(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
BoundMinMax(BoundMinMax) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
BoundOutputter<T> - Class in org.anchoranalysis.io.generator.sequence
An outputter bound together with OutputPattern and a generator.
BoundOutputter(OutputterChecked, OutputPattern, Generator<T>) - Constructor for class org.anchoranalysis.io.generator.sequence.BoundOutputter
 
BoundPhysicalExtent - Class in org.anchoranalysis.mpp.bean.bound
 
BoundPhysicalExtent() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
 
BoundPhysicalExtent(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
 
BoundPhysicalExtent(BoundPhysicalExtent) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
 
BoundReplaceStrategy<T extends FeatureInput,​S extends ReplaceStrategy<T>> - Class in org.anchoranalysis.feature.session.strategy.replace.bind
Attaches a replacement-strategy to a session lazily (i.e.
BoundReplaceStrategy(Function<CacheCreator, S>) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.bind.BoundReplaceStrategy
 
BoundsFromRange<T> - Class in org.anchoranalysis.core.index.bounded
 
BoundsFromRange(GetterFromIndex<T>, BoundedRangeIncomplete) - Constructor for class org.anchoranalysis.core.index.bounded.BoundsFromRange
 
BoundUnitless - Class in org.anchoranalysis.mpp.bean.bound
 
BoundUnitless() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless
 
BoundUnitless(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless
 
BoundUnitless(BoundUnitless) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless
 
box() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
 
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.Mark
 
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
 
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
box(FeatureInputPairMemo, Function<FeatureInputPairMemo, VoxelizedMarkMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
 
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
How we create our scaled masks
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
 
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.Overlay
A bounding-box around the overlay
box(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
Is this other bounding-box FULLY contained within this bounding box?
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.Mark
 
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
Copies a bounding-box area to another Voxels
boxFromBounds(Point3d, double, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator
Calculates a bounding box for a point with a scalar radius in all dimensions
boxFromBounds(Point3d, DoubleMatrix1D, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator
Calculates a bounding box for a point with varying radii in each dimension (that have already been resolved into a matrix)
boxIterator() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
boxList(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
boxList(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
boxList(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
BoxPlot<T> - Class in org.anchoranalysis.plot.index
 
BoxPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, BoxAndWhiskerItem>, GetForSeries<T, Paint>) - Constructor for class org.anchoranalysis.plot.index.BoxPlot
 
BranchChannels - Class in org.anchoranalysis.plugin.io.bean.stack.writer
Uses different raster-writers depending on the number/type of channels.
BranchChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
 
BranchIfDebug<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
Uses one input-manager normally, but a different one if in debug mode
BranchIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
 
BranchStack - Class in org.anchoranalysis.plugin.io.bean.stack.writer
Uses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly 3D.
BranchStack() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
 
bridge(int, H) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
 
bridge(int, H) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithIndex
 
bridge(int, H) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithoutIndex
 
Bridge - Class in org.anchoranalysis.plugin.image.bean.object.match
Matches to another object, and then uses that object to bridge to another
Bridge() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Bridge
 
bridgeElement(int, S) - Method in interface org.anchoranalysis.core.index.BridgeElementWithIndex
 
BridgeElementWithIndex<S,​D,​E extends Exception> - Interface in org.anchoranalysis.core.index
 
buffer() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
The associated buffer for storing the voxels.
buffer(VoxelBuffer<U>, Extent, Function<U, T>, Function<AbstractNativeImg<S, T>, S>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.Wrap
 
BufferedImageFactory - Class in org.anchoranalysis.image.core.stack.bufferedimage
 
BufferedImageOverlay - Class in org.anchoranalysis.image.core.stack.bufferedimage
 
bufferListForSlice(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
 
bufferRel(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
 
bufferValueEqualTo(T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
Checks if the current value from a buffer is equal to a constant value
bufferValueGreaterThan(T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
Checks if the current value from a buffer is greater than a constant value
bv - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
 
byDimension(int) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
 
byDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
byDimension(AxisType) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
 
byDimension(AxisType) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
bySymbol() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
Calculates a feature if only an symbol (ID/name) is known, which refers to another feature.
bySymbol() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
 
ByteRepresentationForChannel - Interface in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
Creates or retrieves a byte representation of the voxels for a particular slice.
bytesForSlice(int) - Method in interface org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.ByteRepresentationForChannel
The byte-representation of the voxels for a particular slice.
bytesPerPixel - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
 
bytesPerPixel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
 
bytesPerPixel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
 
bytesPerPixel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
 

C

cache(CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.cache.CachedSupplier
Creates a cached-version of a CheckedSupplier
cache(StoreSupplier<T>) - Static method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier
Memoizes (caches) the supplied object, and returning it with an identical interface
cache(CheckedProgressingSupplier<T, E>) - Static method in class org.anchoranalysis.core.progress.CachedProgressingSupplier
Creates a cached-version of a CheckedProgressingSupplier
cache(NamedStacksSupplier) - Static method in interface org.anchoranalysis.image.core.stack.NamedStacksSupplier
 
cache(SerializedObjectSupplier<T>) - Static method in interface org.anchoranalysis.io.manifest.finder.SerializedObjectSupplier
 
CACHE_NAME_FIRST - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
CACHE_NAME_MERGED - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
CACHE_NAME_SECOND - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
CacheAndReuseStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.replace
Reuse (without needing to invalidate) an existing session-input as stored in a least-recently used cache, otherwise create a new one.
CacheAndReuseStrategy(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.CacheAndReuseStrategy
 
CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache
 
CacheCreatorSimple - Class in org.anchoranalysis.feature.session.cache.creator
 
CacheCreatorSimple(FeatureList<? extends FeatureInput>, SharedFeatureMulti, FeatureInitParams, Logger) - Constructor for class org.anchoranalysis.feature.session.cache.creator.CacheCreatorSimple
 
CachedProgressingSupplier<T,​E extends Exception> - Class in org.anchoranalysis.core.progress
Memoizes (caches) a call to CheckedProgressingSupplier
CachedSupplier<T,​E extends Exception> - Class in org.anchoranalysis.core.cache
Memoizes (caches) a CheckedSupplier
CachedSupplierBase<T> - Class in org.anchoranalysis.core.cache
Base class for functions that memoize (cache) a call to an interface
CachedSupplierBase() - Constructor for class org.anchoranalysis.core.cache.CachedSupplierBase
 
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
 
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
 
cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
 
cacheResettable(StoreSupplier<T>) - Static method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier
Memoizes (caches) the supplied object, and returning it with a CachedSupplier interface
cachesToAvoidInvalidating() - Method in class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
 
cachesToAvoidInvalidating() - Method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
 
cachesToAvoidInvalidating() - Method in interface org.anchoranalysis.feature.session.strategy.child.FindChildStrategy
If set, these particular-caches are exceptionall NOT invalidated during the typical invalidation operation on their parent.
CacheSupplier<T extends FeatureInput,​E extends Exception> - Interface in org.anchoranalysis.feature.session.strategy.child
 
CacheTransferSource<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.child
An existing cache that can be used as a source for child-caches elsewhere
CacheTransferSource(CacheSupplier<T, OperationFailedException>, Set<ChildCacheName>) - Constructor for class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
 
CacheTransferSourceCollection - Class in org.anchoranalysis.feature.session.strategy.child
 
CacheTransferSourceCollection() - Constructor for class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
 
calc(double, double, double, boolean, boolean) - Static method in class org.anchoranalysis.plugin.operator.feature.score.GaussianScoreCalculator
 
calc(FeatureList<T>, SessionInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCalculator
Calculates a feature-list throwing an exception if there is an error
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
 
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
 
calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
 
calc(SessionInput<T>, FeatureCalculation<U, T>, Function<ResolvedCalculation<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
Calculates a feature using a cached-calculation as delegate, and optional Params return value
calc(FeatureInputObjectCollection) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
 
calc(FeatureInputObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
 
calc(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.AxisRatioEllipsoid
 
calc(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
 
calc(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipsoidicity
 
calc(ObjectMask) - Method in interface org.anchoranalysis.image.feature.evaluator.PayloadCalculator
 
calc(ObjectMask, boolean) - Static method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
 
calc(FeatureInputMarkCollection) - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
 
calc(FeatureInputMarkCollection) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.collection.NumberMarks
 
calc(MemoCollection, EnergySchemeWithSharedFeatures, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
 
calculate(int[]) - Method in class org.anchoranalysis.image.feature.bean.score.VoxelScore
 
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
 
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
 
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
 
calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
 
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.image.bean.spatial.ScaleCalculator
 
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
 
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
 
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
 
calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
 
calculate(Feature<S>, FeatureCalculation<S, T>, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild
Calculates a feature in a child-cache using a new input created from a FeatureCalculation
calculate(Feature<S>, S, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild
Calculates a feature in a child-cache
calculate(Feature<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
Calculates the result of a feature using this input
calculate(Feature<T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
 
calculate(Feature<T>, SessionInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCalculator
Calculate a feature with particular values
calculate(FeatureList<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
Calculates the results of several features using this input
calculate(FeatureList<T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
 
calculate(ChildCacheName, S, Function<CalculationResolver<S>, ResolvedCalculation<U, S>>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild
Calculates a FeatureCalculation in a child-cache
calculate(ResolvedCalculation<S, T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
Calculates a resolved Feature-calculation
calculate(ResolvedCalculation<S, T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
 
calculate(SessionInput<FeatureInput>) - Method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculation
 
calculate(SessionInput<FeatureInputResults>) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
 
calculate(SessionInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
 
calculate(SessionInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
 
calculate(SessionInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
 
calculate(SessionInput<FeatureInputObjectCollection>) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.First
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Merged
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Minimum
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Second
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
 
calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMagnitude
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMIP
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
 
calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipticity
 
calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
 
calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
 
calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
 
calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
 
calculate(SessionInput<FeatureInputMarkCollection>) - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
 
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureMark
 
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
 
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
 
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.MaxRatioRadii
 
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
 
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
 
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
 
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.MarkEllipseCircumEstimate
 
calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.Volume
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsCollection
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsSingleMark
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
 
calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.NumberMarks
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZDistance
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.MinimumDistanceByDimension
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.MinFeatureAsIndividual
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxels
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxelsMask
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
 
calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.BBoxRatio
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MaxSliceArea
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Size
 
calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Constant
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Reference
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Sum
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Maximum
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Mean
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Minimum
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.NormalizedRange
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
 
calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
 
calculate(FeatureCalculation<S, T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
Calculates a feature-calculation after resolving it against the main cache
calculate(FeatureCalculation<S, T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
 
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.Count
 
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
 
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
 
calculate(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
calculate(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
 
calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
 
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
 
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
 
calculate(T) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
Performs one calculation throwing an exception if something goes wrong
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
 
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
 
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
 
calculate(T) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingle
Performs one calculation throwing an exception if something goes wrong
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleChangeInput
 
calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleFromMulti
 
calculate(T) - Method in class org.anchoranalysis.feature.session.SequentialSession
Calculates one params for each feature.
calculate(T, ErrorReporter, boolean) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
 
calculate(T, FeatureList<T>) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
Performs one calculation on a sub-set of the feature list throwing an exception if something goes wrong
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
 
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
 
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
 
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.SequentialSession
 
calculateAcceptanceProb(Kernel<?>, Optional<T>, T, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.AccptProbCalculator
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
 
calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
calculateBound(Point3d, RotationMatrix) - Method in class org.anchoranalysis.mpp.bean.bound.BoundCalculator
 
calculateBound(Point3d, RotationMatrix) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
 
calculateBound(Point3d, RotationMatrix) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
 
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
 
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
 
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
 
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
 
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
 
calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
 
calculateCheckInitialized(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature
 
calculateConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
calculateContext(MarkFactoryContext) - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
calculateCornerMax() - Method in class org.anchoranalysis.spatial.box.BoundingBox
The maximum (right-most) point inside the box.
calculateCornerMaxExclusive() - Method in class org.anchoranalysis.spatial.box.BoundingBox
The maximum (right-most) point just outside the box.
calculateCountNonZero() - Method in class org.anchoranalysis.math.histogram.Histogram
 
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
 
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToFirst
 
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
 
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
 
calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond
 
calculateDensityRatio(double, double, int) - Method in class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
 
CalculateDeriveMarkCollectionInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
 
CalculateDeriveMarkCollectionInput() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
 
CalculateDeriveMarkInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
 
CalculateDeriveMarkInput() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
 
CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
 
CalculateDeriveObjectInput(int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
 
CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element
 
CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
 
CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
 
CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
 
CalculateDilationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
 
CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
 
calculateEccentricity(double, double) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
 
CalculateEllipseLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipse
 
CalculateEllipseLeastSquares() - Constructor for class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
 
CalculateEllipsoidLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
 
CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
 
CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
 
CalculateErosionMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
 
CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
 
calculateFeatureByIdentifier(String, SessionInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator
Searches for a feature that matches a particular identifier
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputObjectCollection>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectCollection
 
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputSingleObject>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObject
 
calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<T>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
 
calculateFeaturesForObjects(ObjectCollection, EnergyStack, CalculateFeaturesForObjects.LabelsForInput<T>) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
 
CalculateFeaturesForObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
 
CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitParamsWithEnergyStack, boolean, InputProcessContext<FeatureTableCalculator<T>>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
 
CalculateFeaturesForObjects.LabelsForInput<T extends FeatureInput> - Interface in org.anchoranalysis.plugin.image.task.feature.calculator
 
calculateForAxis(Dimensions, AxisType) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
 
calculateForAxis(Dimensions, AxisType) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
 
calculateForAxis(Dimensions, AxisType) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize
 
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
 
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
 
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
 
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
 
calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
 
CalculateForChild<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
Performs calculations using child-caches instead of the main cache
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.DotProductOrientationToVector
 
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidAxisRatio
 
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidMaxAreaIntersectingPlane
 
calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
 
calculateForNewMark(VoxelizedMarksWithEnergy, Set<Mark>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
 
calculateForNewMark(MarksFromPartition, Set<Mark>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
 
calculateForNewMark(T, Set<Mark>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
 
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShell
 
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
 
calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
 
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
 
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
 
calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
 
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
 
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
 
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
 
calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
 
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
 
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
 
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
 
calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
 
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
 
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
 
calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
Calculates the result for the specific moment identified by index
CalculateHistogram - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
 
CalculateHistogram(int) - Constructor for class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
 
CalculateHistogramMasked - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
Calculated a histogram for a specific region on a channel, as identified by a mask in another channel
CalculateHistogramMasked(int, int) - Constructor for class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
 
CalculateIncrementalOperationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
 
CalculateIncrementalOperationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
 
CalculateIncrementalOperationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
 
CalculateInputFromDelegate<S,​T extends FeatureInput,​U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate
A base class for Cached-Calculations that generate a Params for feature-calculation using an existing "delegate" calculation
CalculateInputFromDelegate(ResolvedCalculation<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
 
CalculateInputFromDelegate(FeatureCalculation<U, T>, CalculationResolver<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
 
CalculateInputFromDelegateOption<S extends FeatureInput,​T extends FeatureInput,​U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate
Like CalculateInputFromDelegate except assumes optional return value and no parameters
CalculateInputFromDelegateOption(ResolvedCalculation<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
The constructor
CalculateInputFromPair - Class in org.anchoranalysis.image.feature.object.calculation
Calculates a single-input from a pair
CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
 
CalculateInputFromPair.Extract - Enum in org.anchoranalysis.image.feature.object.calculation
 
CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
 
CalculateIntersecting(ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
 
calculateLevel(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
Determines a voxel intensity that can be used for thresholding.
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
 
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
 
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
 
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
 
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
 
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
 
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
 
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
 
CalculateLevel - Class in org.anchoranalysis.image.bean.threshold
Calculates a threshold-level from a histogram.
CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
CalculateLevel() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevel
 
CalculateLevel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
 
CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
CalculateLevelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
 
calculateLevelIncoming(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
 
CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
 
CalculateLevelListBase() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
 
CalculateLevelOne - Class in org.anchoranalysis.image.bean.threshold
 
CalculateLevelOne() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
 
CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
 
CalculateLevelRelativeToThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
 
calculateMaximum() - Method in class org.anchoranalysis.math.histogram.Histogram
Calculates the maximum of the histogram values i.e.
calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator
 
calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator
 
calculateMemoryUsage() - Static method in class org.anchoranalysis.core.system.MemoryUtilities
 
calculateMinimum() - Method in class org.anchoranalysis.math.histogram.Histogram
Calculates the minimum of the histogram values i.e.
calculateMinMax(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds
 
calculateMode() - Method in class org.anchoranalysis.math.histogram.Histogram
 
calculateMode(int) - Method in class org.anchoranalysis.math.histogram.Histogram
Calculates the mode of the histogram values i.e.
calculateNewMaxCurrentValue() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
 
CalculateNumVoxels - Class in org.anchoranalysis.image.feature.object.calculation
 
CalculateNumVoxels(boolean) - Constructor for class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
 
CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
 
CalculateObjectMask(int, ResolvedCalculationMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
 
CalculateObjectMask(CalculateObjectMask) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
Copy constructor
CalculateOverlap - Class in org.anchoranalysis.plugin.mpp.feature.overlap
 
CalculateOverlap(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
 
CalculateOverlapMask - Class in org.anchoranalysis.plugin.mpp.feature.overlap
 
CalculateOverlapMask(int, int, byte) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
 
CalculateOverlapMIP - Class in org.anchoranalysis.plugin.mpp.feature.overlap
 
CalculateOverlapMIP(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
 
CalculateOverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.overlap
 
CalculateOverlapMIPBase(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
 
CalculateOverlapMIPRatio - Class in org.anchoranalysis.plugin.mpp.feature.overlap
 
CalculateOverlapMIPRatio(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
 
calculateOverlapRatio(ObjectMask, ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.OverlapCalculator
 
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
 
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
 
calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
 
calculatePath() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
calculatePath() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
 
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
 
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
 
calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
CalculatePointsFromOutline - Class in org.anchoranalysis.plugin.points.calculate
 
CalculatePointsFromOutline() - Constructor for class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
 
calculateResultsForInput(ProvidesStackInput, InputProcessContext<FeatureList<FeatureInputStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
 
calculateResultsForInput(FileInput, InputProcessContext<FeatureList<FeatureInputHistogram>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
 
calculateResultsForInput(T, InputProcessContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
 
calculateRunningSum(Mask, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.core.mask.IterateVoxelsMask
Calculates the sum and count across voxels intensity that correspond to on voxels on a mask
CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
 
CalculateShellObjectMask(ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
 
calculateSigma(Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.histogram.Mean
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Max
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Min
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StdDev
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
 
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
 
calculateSum() - Method in class org.anchoranalysis.math.histogram.Histogram
 
calculateSumCubes() - Method in class org.anchoranalysis.math.histogram.Histogram
 
calculateSumSquares() - Method in class org.anchoranalysis.math.histogram.Histogram
 
calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
 
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
 
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
 
calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
Performs one calculation recording the error to an ErrorReporter if anything goes wrong, but throwing no exception
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
 
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
 
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
 
calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingle
Performs one calculation recording the error to an ErrorReporter if anything goes wrong, but throwing no exception
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleChangeInput
 
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleFromMulti
 
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.SequentialSession
Calculates the next-object in our sequential series, reporting any exceptions into a reporter log
calculateTemperature(int) - Method in class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
 
calculateTemperature(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
 
calculateTemperature(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.NoAnnealing
 
calculateVolume() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
calculateVolume() - Method in class org.anchoranalysis.spatial.Extent
 
calculateVolumeAsInt() - Method in class org.anchoranalysis.spatial.Extent
 
calculateWith(Feature<T>, T, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
Starts a feature-session for a single feature - and performs a calculation
calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
 
calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
 
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels
 
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxelFaces
 
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxels
 
calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
 
calculateWithParameters(ObjectMask, OutlineKernelParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
 
calculateWithParameters(ObjectMask, OutlineKernelParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
 
calculateWithParameters(ObjectMask, OutlineKernelParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
 
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
 
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
 
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
 
calculateZScore(double, double, double) - Static method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
 
CalculationResolver<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
Searches a cache to reuses a FeatureCalculation if it already exists.
calculator() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
A means of calculating feature values using this cache.
calculator() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
 
calculator() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
 
calculatorForAll(FeatureList<T>) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
Calculates all image-features in the feature-store
calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
Calculates a single-feature that comes from a provider (but can reference the other features from the store)
call() - Method in class org.anchoranalysis.experiment.task.processor.CallableJob
 
call(CheckedSupplier<T, E>) - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
 
CallableJob<T extends InputFromManager,​S> - Class in org.anchoranalysis.experiment.task.processor
A job derived from a Task that can be placed on different threads
CallableJob(Task<T, S>, ParametersUnbound<T, S>, JobState, JobDescription, ConcurrentJobMonitor, Optional<MessageLogger>, int) - Constructor for class org.anchoranalysis.experiment.task.processor.CallableJob
Constructor
callChannelIfSupported(int, BiConsumer<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>>, Consumer<Channel>) - Method in class org.anchoranalysis.image.core.stack.ChannelMapper
 
callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.IterateVoxelsNeighbors
Iterate over each point in the neighborhood of an existing point.
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.path.RootPath
 
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
 
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
 
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
 
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
 
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
 
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
 
canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
canEqual(Object) - Method in class org.anchoranalysis.core.concurrency.WithPriority
 
canEqual(Object) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
 
canEqual(Object) - Method in class org.anchoranalysis.core.index.Indexable
 
canEqual(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
 
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
 
canEqual(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
 
canEqual(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
 
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
 
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
 
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
 
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
 
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
 
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
 
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
 
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
 
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
 
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
 
canEqual(Object) - Method in class org.anchoranalysis.image.feature.stack.FeatureInputStack
 
canEqual(Object) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
 
canEqual(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
canEqual(Object) - Method in class org.anchoranalysis.overlay.IndexableOverlays
 
canEqual(Object) - Method in class org.anchoranalysis.plot.AxisLimits
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
 
canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
 
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3d
 
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3f
 
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3i
 
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Vector3d
 
canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
 
canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
 
canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
 
canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
 
canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
 
canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
 
canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
 
canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
 
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
The capacity of the buffer ala Buffer.capacity.
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
The capacity (i.e.
castTo() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
Casts voxels to a particular type
Cell - Class in org.anchoranalysis.image.bean.spatial.arrange
 
Cell() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Cell
 
centerOfGravity() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Calculates center-of-gravity across all axes
centerOfGravity() - Method in class org.anchoranalysis.spatial.box.BoundingBox
Similar to BoundingBox.midpoint() but not always identical.
centerOfGravity(AxisType) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Calculates center-of-gravity for one specific axis only
CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single
 
CenterOfGravity() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
 
CenterOfGravity(AxisType) - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
Creates for a specific axis.
CenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
 
CenterOnMask() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
 
centerPoint() - Method in class org.anchoranalysis.mpp.mark.Mark
 
centerPoint() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
 
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
centerPoint() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
CenterSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
 
CenterSlice() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
 
CenterSliceBase - Class in org.anchoranalysis.plugin.mpp.bean.region
 
CenterSliceBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
 
CenterSliceWindow - Class in org.anchoranalysis.plugin.mpp.bean.region
Like {#link org.anchoranalysis.plugin.mpp.bean.region.CenterSlice} but considers more than one slice, specifically centerSlice+- windowSize
CenterSliceWindow() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
 
chainCode(int, int, int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
 
chainCodes(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
Decodes a chain-code into a point
ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
Maps directions to chain codes
CHANGE_EXISTING_CHANNEL - org.anchoranalysis.image.core.channel.convert.ConversionPolicy
 
ChangeableOutputSequence<T,​S> - Class in org.anchoranalysis.plugin.image.task.bean.format
 
ChangeableOutputSequence() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
 
changedMarkIDArray() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
The mark ids that were changed in the last energy calculation for the kernel
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
 
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
 
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
 
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
 
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
 
changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
changedOffset(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
changeExtent(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
changeExtentZ(int) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
changeInput(U) - Method in class org.anchoranalysis.experiment.task.InputBound
Immutably changes the input-object
changeIntensity(Voxels<?>, IntUnaryOperator) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Changes each voxel, reading and writing the buffer as an int.
changePrefix(DirectoryWithPrefix) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
Creates a new OutputterTarget with a changed prefix.
changePrefix(DirectoryWithPrefix, Optional<WriteOperationRecorder>) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
Creates a OutputterChecked with a changed prefix and WriteOperationRecorder.
changeZ(int, int) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
channel() - Method in class org.anchoranalysis.image.core.mask.Mask
The underlying channel which contains the binary-values.
channel(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
 
Channel - Class in org.anchoranalysis.image.core.channel
A channel from an image.
Channel(Voxels<?>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.channel.Channel
Constructor
channelAt(int) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
ChannelConverter<T> - Class in org.anchoranalysis.image.core.channel.convert
Converts a channel from one type to another specific type.
ChannelConverter(VoxelDataType, VoxelsConverter<T>, VoxelsFactoryTypeBound<T>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ChannelConverter
 
ChannelConverterAttached<S,​T> - Interface in org.anchoranalysis.image.core.channel.convert.attached
A channel-converter that has been permanently attached to a particular object.
ChannelConverterMulti - Class in org.anchoranalysis.image.core.channel.convert
Converts a channel from one type to multiple other types.
ChannelConverterMulti() - Constructor for class org.anchoranalysis.image.core.channel.convert.ChannelConverterMulti
 
ChannelConvertStyle - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
Converts a channel(s) at a particular timepoint into a stack(s).
ChannelConvertStyle() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle
 
ChannelFactory - Class in org.anchoranalysis.image.core.channel.factory
Creates a channel for one of several data-types
ChannelFactoryByte - Class in org.anchoranalysis.image.core.channel.factory
 
ChannelFactoryByte() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryByte
 
ChannelFactoryFloat - Class in org.anchoranalysis.image.core.channel.factory
 
ChannelFactoryFloat() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryFloat
 
ChannelFactoryInt - Class in org.anchoranalysis.image.core.channel.factory
 
ChannelFactoryInt() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryInt
 
ChannelFactoryShort - Class in org.anchoranalysis.image.core.channel.factory
 
ChannelFactoryShort() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryShort
 
ChannelFactorySingleType - Class in org.anchoranalysis.image.core.channel.factory
Creates a channel for a specific data-type
ChannelFactorySingleType(VoxelDataType, VoxelsFactoryTypeBound<?>) - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
 
ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.channel
 
ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class org.anchoranalysis.plugin.image.task.channel.ChannelGetterForTimepoint
 
ChannelMapper - Class in org.anchoranalysis.image.core.stack
Helps a retrieve channel and an associated converter and apply operation on them jointly
ChannelMapper(IntFunction<Channel>, IntFunction<Optional<ChannelConverterAttached<Channel, UnsignedByteBuffer>>>) - Constructor for class org.anchoranalysis.image.core.stack.ChannelMapper
 
channelNames() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
 
channelNames() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
ChannelProvider - Class in org.anchoranalysis.image.bean.provider
 
ChannelProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProvider
 
ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider
A channel-provider based-on two input channel-providers that must be of the same dimensionality
ChannelProviderBinary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
 
ChannelProviderTernary - Class in org.anchoranalysis.image.bean.provider
 
ChannelProviderTernary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
 
ChannelProviderUnary - Class in org.anchoranalysis.image.bean.provider
 
ChannelProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
 
channels() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped
Source of channels for aggregating.
ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
 
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
 
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
 
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
 
channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
check(Channel, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
Checks a channel to make sure it's the same size as an an existing channel
check(Channel, Mask) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
 
check(Mask, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
Checks a channel to make sure it's the same size as an an existing channel
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.bean.mark.CheckMark
Checks a mark
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
 
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AnySliceCenterOnMask
 
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
 
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.EllipseBoundsCheck
 
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
 
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
 
check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
 
check(T) - Static method in class org.anchoranalysis.test.experiment.BeanTestChecker
Checks if a bean has all necessary items, throwing a run-time exception if it does not.
Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
 
Check() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
 
Check() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
 
checkAndInit(T, P, Logger) - Static method in class org.anchoranalysis.test.experiment.BeanTestChecker
Checks if a bean has all necessary items as with BeanTestChecker.check(T) and also initializes the bean.
CheckCacheForSpecificChildren - Class in org.anchoranalysis.feature.session.strategy.child
For particular child-caches, check if a session-input is available from another LRU-cache and reuse.
CheckCacheForSpecificChildren(Class<?>, CacheTransferSourceCollection) - Constructor for class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
 
checkChannelType(VoxelDataType) - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
Checks that a channel has the same type (max value) as the others
checkCompatibleWith(Mark) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
CheckedBiConsumer<S,​T,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like BiConsumer but can also throw a checked exception.
CheckedBiFunction<S,​T,​V,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like BiFunction but can also throw a checked exception.
CheckedBooleanSupplier<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like BooleanSupplier but can also throw an exception.
CheckedConsumer<S,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Consumes a value and throws an exception
CheckedFunction<S,​V,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like Function but can also thrown an exception.
CheckedIntConsumer<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Consumes an int and throws an exception
CheckedIntFunction<T,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like IntFunction but can also thrown an exception.
CheckedPredicate<T,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like Predicate but can also throw an exception.
CheckedProgressingSupplier<R,​E extends Exception> - Interface in org.anchoranalysis.core.progress
Like CheckedSupplier but can update a progress-reporter as the operation progresses.
CheckedRunnable<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
 
CheckedStream - Class in org.anchoranalysis.core.functional
Map operations for streams that can throw checked-exceptions
CheckedStream.ConvertedToRuntimeException - Exception in org.anchoranalysis.core.functional
An exception that wraps another exception, but exposes itself as a RuntimeException
CheckedSupplier<T,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like Supplier but can also throw an exception.
CheckedToDoubleBiFunction<T,​U,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like ToDoubleBiFunction but can also thrown an exception.
CheckedToIntFunction<S,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like ToIntFunction but can also thrown an exception.
CheckedUnaryOperator<T,​E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
Like a UnaryOperator but allows an exception to be thrown
CheckException - Exception in org.anchoranalysis.mpp.feature.error
 
CheckException(String) - Constructor for exception org.anchoranalysis.mpp.feature.error.CheckException
 
CheckException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.feature.error.CheckException
 
CheckException(Throwable) - Constructor for exception org.anchoranalysis.mpp.feature.error.CheckException
 
checkExtentMatch(BoundingBox, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.ExtentMatchHelper
 
CheckIfAllowed - Class in org.anchoranalysis.io.output.writer
Only allows outputs, if the output-name is allowed in the OutputterChecked.
CheckIfAllowed(SingleLevelOutputEnabled, Optional<WriterExecuteBeforeEveryOperation>, Writer) - Constructor for class org.anchoranalysis.io.output.writer.CheckIfAllowed
 
checkIfConnected() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Determines if an object-mask is connected.
CheckMark - Class in org.anchoranalysis.mpp.feature.bean.mark
A predicate on a mark to check if a condition has been satisfied.
CheckMark() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.CheckMark
 
CheckMarkWithMask - Class in org.anchoranalysis.plugin.mpp.bean.check
 
CheckMarkWithMask() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.bean.AnchorBean
Checks that a bean's properties conform to expectations.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
 
checkMisconfigured(BeanInstanceMap) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
CheckMisconfigured - Class in org.anchoranalysis.bean.initializable
Routines for checking that particular patterns exist with bean-properties
CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.groupfiles.check
 
CheckParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.check.CheckParsedFilePathBag
 
checkResultVector(ResultsVector) - Static method in class org.anchoranalysis.test.feature.ConstantsInListFixture
checks that a result-vector has the results we expect from the feature-list associated with this fixture
checkSize(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
 
checkUnsupported3D(Channel) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
 
checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
 
checkUnsupportedSeeds(Optional<SeedCollection>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
 
childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
Gets/creates a child-cache for a given name
childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
 
childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
 
childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
 
childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
 
childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in interface org.anchoranalysis.feature.session.strategy.child.FindChildStrategy
Selects a child-cache given a parent and a child-name
ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache
A unique identifier for a child-cache name, that uses a class and optionally additionally a part-name a class: guaranteed to be unique for the class an optional part-name (string): a further division of the class into different caches
ChildCacheName(Class<?>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName
Uses only the class as an identifier - and a blank part-name
ChildCacheName(Class<?>, int) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName
Uses only the class as an identifier - and a integer part-name
ChildCacheName(Class<?>, String) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName
Uses both the class and a part-name as an identifier
children() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
ChooseOneList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
ChooseOneList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ChooseOneList
 
Circle - Class in org.anchoranalysis.mpp.mark.conic
A circle
Circle() - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle
 
Circle(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle
Creates with a radius within particular bounds.
Circle(Circle) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle
Copy constructor
circleAt(Point2i, double) - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture
 
CircleObjectFixture - Class in org.anchoranalysis.test.feature.plugins.objects
 
circumference(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
classificationString(boolean) - Static method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
 
classInCurrentJar() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
a class which we use to determine the base location for pathRelativeProperties
clean() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
clean() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
cleanUp() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
 
cleanUp(VoxelPartitionFactory<Histogram>) - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
 
cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
 
cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
 
cleanUp(VoxelPartitionFactory<T>) - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
 
clear() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
clear() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
clear() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Clears the buffer ala Buffer.clear().
clear() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
clear() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
clearBest() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
 
clearVisualizationState() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
 
clearVisualizationState() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
 
clearVisualizationState() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
clip(Point3d, Dimensions) - Static method in class org.anchoranalysis.mpp.points.PointClipper
 
clip(Point3i, Dimensions) - Static method in class org.anchoranalysis.mpp.points.PointClipper
 
ClipHistogramMax - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
Clips the input-histogram to a certain maximum value, and then delegates the calculate-level.
ClipHistogramMax() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
 
clipTo(Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Makes sure an object fits inside an extent, removing any parts which do not.
clipTo(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
clipTo(T, Extent) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
Ensures the element lies within a certain extent.
close() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
 
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
 
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
 
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterMultiple
 
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
 
close() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
 
close() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
Closes any open file-handles.
close() - Method in class org.anchoranalysis.feature.io.results.ResultsWriter
 
close() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
 
close() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
 
close() - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
 
close() - Method in class org.anchoranalysis.plugin.image.task.slice.SharedStateSelectedSlice
 
close() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
close(boolean) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
 
close(boolean) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
 
close(boolean) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
 
close(boolean) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
 
close(boolean) - Method in interface org.anchoranalysis.experiment.log.StatefulMessageLogger
 
close(boolean) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
 
close(ErrorReporter) - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
 
close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
 
close(ErrorReporter) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
close(ErrorReporter) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
 
close(ErrorReporter) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
 
closeAnyOpenIO() - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
 
closeAnyOpenIO() - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
 
closestPointOnBorder(Point3d) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
CODE_MINIMA - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
CODE_PLATEAU - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
CODE_TEMPORARY - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
CODE_UNVISITED - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
CoefficientOfVarianceFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
 
CoefficientOfVarianceFromAll() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
 
coefficientOfVariation(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics
 
CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
CoefficientOfVariation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
 
CollapseFileName - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive
Takes a file-path of form somedir/somename.ext and converts to somedir.ext
CollapseFileName() - Constructor for class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
 
CollectionGenerator<T> - Class in org.anchoranalysis.io.generator.collection
Writes a collection of elements as a subdirectory with each element as a single file in the subdirectory.
CollectionGenerator(Generator<T>, String) - Constructor for class org.anchoranalysis.io.generator.collection.CollectionGenerator
 
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked
Collects the result of the operation after processing neighbor pixels
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor
Collects the result of the operation after processing neighbor pixels
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute
Collects the result of the operation after processing neighbor pixels
collectResult() - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
 
colorAxis(Axis) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
colorChart(JFreeChart) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
ColorConverterBase - Class in org.anchoranalysis.plugin.opencv.bean.stack.provider.color
Converts a RGB stack into another color space using OpenCV
ColorConverterBase() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ColorConverterBase
 
ColoredBase - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
Base class for providers that draw entities (an outline or filled) on a background
ColoredBase() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
 
ColoredBaseWithGenerator - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
Like ColoredBase but uses a generator to determine the colors for the objects
ColoredBaseWithGenerator() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
 
ColoredMarks - Class in org.anchoranalysis.mpp.mark
 
ColoredMarks - Class in org.anchoranalysis.plugin.mpp.bean.stack.provider
Draws a colored representation (outline or filled) of an MarkCollection on a background
ColoredMarks() - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
 
ColoredMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
 
ColoredMarks(MarkCollection, ColorIndex, IdentifierGetter<Mark>) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
 
ColoredMarks(MarkCollection, ColorList) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
 
ColoredMarks(Mark, RGBColor) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
 
ColoredMarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
 
ColoredMarksWithDisplayStack(MarksWithDisplayStack, ColorIndex, IdentifierGetter<Mark>) - Constructor for class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
ColoredMarksWithDisplayStack(ColoredMarks, DisplayStack) - Constructor for class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
ColoredMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
Draws a colored representation (outline or filled) of a ObjectMask on a background
ColoredMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
 
ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object
Associates a ColorList with a ObjectCollection
ColoredObjectCollection() - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
Create with an empty collection.
ColoredObjectCollection(ObjectCollection, ColorList) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
Create with an existing object and color list.
ColoredObjectCollection(ObjectMask, RGBColor) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
Create with a single object and color.
ColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
Draws a colored representation (outline or filled) of an ObjectCollection on a background
ColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
 
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
Creates colored-objects to be drawn
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
 
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
 
coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
 
ColoredOverlayCollection - Class in org.anchoranalysis.overlay.collection
 
ColoredOverlayCollection() - Constructor for class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
ColoredOverlayCollection(OverlayCollection, ColorList) - Constructor for class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
colorFor(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
A color for a particular object
colorForEachIndex(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorScheme
Assigns a color to each index value from a list of size numberColors.
ColorIndex - Interface in org.anchoranalysis.core.color
 
ColorIndexModulo - Class in org.anchoranalysis.core.color
 
ColorIndexModulo(ColorIndex) - Constructor for class org.anchoranalysis.core.color.ColorIndexModulo
 
colorLegend(LegendTitle) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
ColorList - Class in org.anchoranalysis.core.color
 
ColorList() - Constructor for class org.anchoranalysis.core.color.ColorList
 
ColorList(Color...) - Constructor for class org.anchoranalysis.core.color.ColorList
 
ColorList(RGBColor) - Constructor for class org.anchoranalysis.core.color.ColorList
 
ColorList(RGBColor...) - Constructor for class org.anchoranalysis.core.color.ColorList
 
colorPlot(CategoryPlot) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
colorPlot(XYPlot) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
ColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator
 
ColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.ColorPool
 
ColorProvider - Class in org.anchoranalysis.image.bean.provider
Provides a list of one or more colors
ColorProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ColorProvider
 
ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme
Creates a set of related colors.
ColorScheme() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorScheme
 
ColorSchemeUnary - Class in org.anchoranalysis.bean.shared.color.scheme
Like ColorScheme but employs a unary operator on a call to an existing ColorScheme.
ColorSchemeUnary() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
 
ColorSchemeUnary(ColorScheme) - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
 
colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ColorConverterBase
The color space conversion code to use from OpenCV
colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToHSV
 
colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToLab
 
column(int) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
ColumnDefinition - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
 
ColumnDefinition() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
 
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
 
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
 
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
 
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd
 
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
 
combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelOr
 
combine(Path, Path) - Static method in class org.anchoranalysis.bean.xml.factory.BeanPathUtilities
 
Combine - Class in org.anchoranalysis.plugin.io.bean.provider.file
 
Combine() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.Combine
 
CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
 
CombineBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
 
CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task
 
CombineCSV() - Constructor for class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
combined() - Method in class org.anchoranalysis.core.system.path.PathDifference
The directory-component (if it exists) and filename-component combined.
combined() - Method in class org.anchoranalysis.core.system.path.SplitPath
 
CombinedListGenerator<T> - Class in org.anchoranalysis.io.generator.combined
Several generators combined together with a common element-type.
CombinedListGenerator(Stream<NameValue<Generator<T>>>) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
 
CombinedListGenerator(NameValue<Generator<T>>) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
 
CombinedListGenerator(Generator<T>...) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
 
CombinedName - Class in org.anchoranalysis.feature.io.name
A name which is unique when a primaryName is combined with a secondaryName
CombinedName(String, String) - Constructor for class org.anchoranalysis.feature.io.name.CombinedName
Creates with explicit strings for both parts.
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
 
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
 
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
 
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
 
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
 
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
 
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
 
combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
 
combineDscrsRecursively(String, String) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
Traverses through a set of nested-exceptions creating a description for each "combined" exception, and combining them into a single string.
CombineObjectsForFeatures<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine
A way to combine (or not combine) objects so that they provide a feature-table.
CombineObjectsForFeatures() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
 
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
 
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
 
combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
 
combineToOnePath() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
Combines all the contiguous paths to a single-path
combineToOnePath(List<ContiguousVoxelPath>) - Static method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.CombineToOnePath
Combines all the contiguous paths to a single-path
CombineToOnePath - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine
 
combineTypes(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.CombineTypes
 
CombineTypes - Class in org.anchoranalysis.image.voxel.datatype
 
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
 
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
 
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
 
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
 
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
 
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
 
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
 
combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
 
CommandLineException - Exception in org.anchoranalysis.launcher
An exception thrown at run-time while processing command-line args
CommandLineException(String) - Constructor for exception org.anchoranalysis.launcher.CommandLineException
 
CommandLineExtracter - Class in org.anchoranalysis.launcher.options
Adds methods to CommandLine for querying and extracting options, with and without arguments.
CommandLineExtracter(CommandLine) - Constructor for class org.anchoranalysis.launcher.options.CommandLineExtracter
 
CommandLineOptions - Class in org.anchoranalysis.launcher.options
All command-line options used by the launcher.
common() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
Creates a CommonContext a context that contains a subset of this context.
CommonContext - Class in org.anchoranalysis.core.log
A logger with additional configuration that are coupled together widely in the code
CommonContext(Logger, Path) - Constructor for class org.anchoranalysis.core.log.CommonContext
 
commonType(Stream<VoxelDataType>) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType
Finds a common type to represent (ideally without loss of precision} of a stream of types.
commonType(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType
Finds a common type to represent (ideally without loss of precision} both first and second.
Comparator3d<T extends Tuple3d> - Class in org.anchoranalysis.spatial.point
 
Comparator3d() - Constructor for class org.anchoranalysis.spatial.point.Comparator3d
 
Comparator3i<T extends Tuple3i> - Class in org.anchoranalysis.spatial.point
 
Comparator3i() - Constructor for class org.anchoranalysis.spatial.point.Comparator3i
 
ComparatorOrderByName<V> - Class in org.anchoranalysis.core.identifier.name
Orders two name-values by their name (alphabetic order from standard String.compareTo(String))
ComparatorOrderByName() - Constructor for class org.anchoranalysis.core.identifier.name.ComparatorOrderByName
 
compare(NameValue<V>, NameValue<V>) - Method in class org.anchoranalysis.core.identifier.name.ComparatorOrderByName
 
compare(T, T) - Method in class org.anchoranalysis.spatial.point.Comparator3d
 
compare(T, T) - Method in class org.anchoranalysis.spatial.point.Comparator3i
 
CompareAnnotations<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
Task to compare a set of annotations to a segmentation or other set of annotations.
CompareAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
Comparer - Class in org.anchoranalysis.annotation.io.bean.comparer
 
Comparer() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.Comparer
 
compareTo(WithPriority<T>) - Method in class org.anchoranalysis.core.concurrency.WithPriority
Orders so that hasPriority==true has higher priority in queue to hasPriority==false
compareTo(IndexGetter) - Method in class org.anchoranalysis.core.index.Indexable
 
compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.CombinedName
 
compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.SimpleName
 
compareTo(EigenvalueAndVector) - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
 
compareTo(WithConfidence<T>) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
 
compareTo(SortedSetChannel) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
 
compareTo(SortedSetSlice) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
 
CompareWithRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
Compares a value with a range, returning specified constants if its inside the range, below it or above it
CompareWithRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
 
CompareWithRangeFeature<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range.feature
Like CompareWithRange but uses features to calculate boundary values
CompareWithRangeFeature() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
 
CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark
 
Compose<S,​T,​U> - Class in org.anchoranalysis.mpp.segment.transformer
Combines a transformation from S to U with one from U to T
Compose() - Constructor for class org.anchoranalysis.mpp.segment.transformer.Compose
 
Compose(StateTransformerBean<S, U>, StateTransformerBean<U, T>) - Constructor for class org.anchoranalysis.mpp.segment.transformer.Compose
 
CompressTIFF - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
 
CompressTIFF() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CompressTIFF
 
computeInitialFeasibleSolution() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
Compute an initial feasible solution by assigning zero labels to the workers and by assigning to each job a label equal to the minimum cost among its incident edges.
Concatenate - Class in org.anchoranalysis.bean.define.adder
Concatenates a list of adders
Concatenate - Class in org.anchoranalysis.plugin.image.bean.color.provider
 
Concatenate - Class in org.anchoranalysis.plugin.image.bean.object.provider
 
Concatenate - Class in org.anchoranalysis.plugin.image.bean.stack.provider
Combines all the channels from one or more sources (stacks, channels etc.)
Concatenate<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
Concatenates several input-managers
Concatenate() - Constructor for class org.anchoranalysis.bean.define.adder.Concatenate
 
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
 
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
 
Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
 
Concatenate() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Concatenate
 
ConcatenateFileTypes - Class in org.anchoranalysis.io.generator
Concatenates the arrays of FileType that may be returned from write operations.
ConcatenateFileTypes() - Constructor for class org.anchoranalysis.io.generator.ConcatenateFileTypes
Creates to always use a list for tracking.
ConcatenateFileTypes(boolean) - Constructor for class org.anchoranalysis.io.generator.ConcatenateFileTypes
Create to use a list for tracking if a flag is true, otherwise to just remember the last result of each call to ConcatenateFileTypes.add(org.anchoranalysis.io.manifest.file.FileType[]).
ConcurrencyPlan - Class in org.anchoranalysis.core.concurrency
How many allocated CPUS and CPUs can be used.
ConcurrentJobMonitor - Class in org.anchoranalysis.experiment.task.processor
 
ConcurrentJobMonitor(long) - Constructor for class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
ConcurrentModelException - Exception in org.anchoranalysis.core.concurrency
This exception indicates that an error occurred when performing inference from a model concurrently.
ConcurrentModelException(Throwable) - Constructor for exception org.anchoranalysis.core.concurrency.ConcurrentModelException
 
ConcurrentModelPool<T> - Class in org.anchoranalysis.core.concurrency
Keeps concurrent copies of a model to be used by different threads.
ConcurrentModelPool(ConcurrencyPlan, ConcurrentModelPool.CreateModelForPool<T>) - Constructor for class org.anchoranalysis.core.concurrency.ConcurrentModelPool
 
ConcurrentModelPool.CreateModelForPool<T> - Interface in org.anchoranalysis.core.concurrency
Creates a model to use in the pool
ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel
 
ConditionalKernel(BinaryKernel, int, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
 
ConditionallyMergeOverlappingObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
Where objects overlap, they are merged together if certain conditions are fulfilled.
ConditionallyMergeOverlappingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
 
ConfigureBioformatsLogging - Class in org.anchoranalysis.io.bioformats
Singleton class for making sure Bioformats is configured configured.
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
 
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
 
ConicBase - Class in org.anchoranalysis.mpp.mark.conic
 
ConicBase() - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase
 
ConicBase(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase
 
ConicFitterBase - Class in org.anchoranalysis.plugin.points.bean.fitter
 
ConicFitterBase() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
ConnectedComponentsFromBinarySegmentation - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
Performs a binary-segmentation of the channel and converts its connected-components into objects
ConnectedComponentsFromBinarySegmentation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
 
ConnectedComponentsFromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
Converts a binary-mask into its connected components
ConnectedComponentsFromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
 
ConnectedComponentUnionFind - Class in org.anchoranalysis.image.voxel.object.factory.unionfind
 
ConnectedComponentUnionFind(int, boolean) - Constructor for class org.anchoranalysis.image.voxel.object.factory.unionfind.ConnectedComponentUnionFind
 
connectedTo(Contour) - Method in class org.anchoranalysis.spatial.Contour
 
connectedToFirstPointOf(Contour) - Method in class org.anchoranalysis.spatial.Contour
 
connectedToLastPointOf(Contour) - Method in class org.anchoranalysis.spatial.Contour
 
considerVisit(Point3i, int) - Method in interface org.anchoranalysis.image.core.outline.traverser.ConsiderVisit
 
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
 
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
 
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
 
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
 
considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
 
ConsiderVisit - Interface in org.anchoranalysis.image.core.outline.traverser
 
ConsistentChannelChecker - Class in org.anchoranalysis.plugin.image.task.grouped
Checks that the histograms created from channels all have the same data type, res, max-value etc.
ConsistentChannelChecker() - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
 
ConsoleAccepted - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
ConsoleAccepted() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
 
ConsoleAggregatedReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
ConsoleAggregatedReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
 
ConsoleAggregatedReporter(double) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
 
ConsoleMessageLogger - Class in org.anchoranalysis.experiment.log
 
ConsoleMessageLogger() - Constructor for class org.anchoranalysis.experiment.log.ConsoleMessageLogger
 
Constant<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
 
Constant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
A constant value for thresholding
Constant - Class in org.anchoranalysis.plugin.io.bean.path.derive
Always generates a constant path irrespective of the the input
Constant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
 
Constant() - Constructor for class org.anchoranalysis.feature.bean.operator.Constant
 
Constant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
 
Constant() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
 
Constant() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
 
Constant(double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant
Constructor with a particular value
Constant(int) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
 
Constant(String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
 
Constant(String, double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant
Constructor with a particular value and a custom-name
ConstantBoundGenerator - Class in org.anchoranalysis.plugin.mpp.bean.bound
 
ConstantBoundGenerator() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
 
ConstantBoundGenerator(ResolvedBound) - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
 
ConstantsInListFixture - Class in org.anchoranalysis.test.feature
 
ConstantToThePowerOf<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
ConstantToThePowerOf() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
 
ConstantWeight - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
All marks have weight of 1
ConstantWeight() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ConstantWeight
 
containerOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
 
containerRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
 
contains() - Method in class org.anchoranalysis.spatial.box.BoundingBox
For evaluating whether this bounding-box contains other points, boxes etc.?
contains(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
contains(int, int, int) - Method in class org.anchoranalysis.spatial.Extent
 
contains(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
contains(Object) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
contains(String) - Method in interface org.anchoranalysis.bean.StringBeanCollection
 
contains(String) - Method in class org.anchoranalysis.bean.StringList
 
contains(String) - Method in class org.anchoranalysis.bean.StringSet
 
contains(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
 
contains(ChildCacheName) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
 
contains(BoundingBox) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
contains(BoundingBox) - Method in class org.anchoranalysis.spatial.Extent
 
contains(Point2i) - Method in class org.anchoranalysis.spatial.Extent
 
contains(Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
contains(Point3d) - Method in class org.anchoranalysis.spatial.Extent
 
contains(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
 
contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
contains(Point3i) - Method in class org.anchoranalysis.spatial.rtree.RTree
Which bounding-boxes contain a particular point.
contains(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
 
containsAll(Collection<?>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
containsChild(ChildCacheName) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
 
containsKey(Class<?>) - Method in class org.anchoranalysis.bean.BeanInstanceMap
 
containsKey(Object) - Method in class org.anchoranalysis.core.value.KeyValueParams
 
containsKey(String) - Method in class org.anchoranalysis.core.value.KeyValueParams
 
containsMark(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
containsVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
Does the graph contain a particular vertex?
containsX(double) - Method in class org.anchoranalysis.spatial.Extent
 
containsX(int) - Method in class org.anchoranalysis.spatial.Extent
 
containsY(double) - Method in class org.anchoranalysis.spatial.Extent
 
containsY(int) - Method in class org.anchoranalysis.spatial.Extent
 
containsZ(double) - Method in class org.anchoranalysis.spatial.Extent
 
containsZ(int) - Method in class org.anchoranalysis.spatial.Extent
 
context() - Method in class org.anchoranalysis.experiment.task.InputBound
 
ContiguousVoxelPath - Class in org.anchoranalysis.image.core.outline.traverser.path
A list of visited pixels which forms one contiguous path (each voxel neighbors each other)
ContiguousVoxelPath() - Constructor for class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
Without any connection-point
ContiguousVoxelPath(Point3i, Point3i) - Constructor for class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
With a single initial-point, and maybe a connection point
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationCondition
 
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
 
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TriggerTerminationCondition
 
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
 
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
 
continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
 
Contour - Class in org.anchoranalysis.spatial
A path of successively-neighbored points.
Contour() - Constructor for class org.anchoranalysis.spatial.Contour
 
ContourList - Class in org.anchoranalysis.plugin.points.contour
 
ContourList() - Constructor for class org.anchoranalysis.plugin.points.contour.ContourList
 
contoursForObject(ObjectMask) - Static method in class org.anchoranalysis.plugin.opencv.CVFindContours
 
ConversionPolicy - Enum in org.anchoranalysis.image.core.channel.convert
 
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
 
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
 
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
 
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
 
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
 
convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
 
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle
Converts a particular set of channels.
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
 
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
 
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
 
convert(Channel, ConversionPolicy) - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached
 
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
 
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
 
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
 
convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter
 
convert(Channel, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverterMulti
 
convert(Stack, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter
 
Convert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
Converts a channel by applying a converter (no histogram is involved in the conversion).
Convert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
 
convert2iTo3d(List<Point2i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
convert2iTo3f(List<Point2i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
convert3dTo3f(List<Point3d>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
convert3fTo3d(List<Point3f>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
convert3i(List<Point3d>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
convert3i(List<Point3f>, boolean) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
convert3iTo3f(List<Point3i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
ConvertBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
 
ConvertBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
 
ConvertChannelsInputToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
An input object that converts NamedChannelsInput to StackSequenceInput
ConvertChannelsInputToStack(NamedChannelsInput) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
 
ConvertChannelsInputToStack(NamedChannelsInput, int, Optional<String>) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
 
ConvertChannelTo - Class in org.anchoranalysis.image.bean.channel.converter
Converts a channel from one type to another
ConvertChannelTo() - Constructor for class org.anchoranalysis.image.bean.channel.converter.ConvertChannelTo
 
ConvertChannelToWithHistogram - Class in org.anchoranalysis.image.bean.channel.converter
 
ConvertChannelToWithHistogram() - Constructor for class org.anchoranalysis.image.bean.channel.converter.ConvertChannelToWithHistogram
 
convertCode(int, int, EncodedVoxels, Point3i) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
Convert code to connected-component
ConvertedToRuntimeException(Throwable) - Constructor for exception org.anchoranalysis.core.functional.CheckedStream.ConvertedToRuntimeException
 
convertFloat(FloatBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
 
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
 
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
 
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
 
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
 
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Copies a value from the current position in a FloatBuffer to the current position in a buffer of type T.
convertFrom(VoxelsWrapper, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Creates a new voxels of type T and copies the voxels from from.
ConvertFromImagePlus - Class in org.anchoranalysis.io.imagej.convert
Converts an ImagePlus into a channel or voxels.
ConvertFromMat - Class in org.anchoranalysis.plugin.opencv.convert
 
ConvertFromPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
converts a feature to a physical distance in a XY place that is isometric
ConvertFromPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertFromPhysicalVolume
 
convertFromUnits(double, String) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
Converts a value from another unit-type to base units.
convertFromUnits(double, SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
Converts a value from another unit-type to base units.
ConvertImageFormat - Class in org.anchoranalysis.plugin.image.task.bean.format
Converts each input-image to the default output format, optionally changing the bit depth.
ConvertImageFormat() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
 
convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
 
convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
 
convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
 
ConvertNamedChannels<T extends NamedChannelsInput,​S,​U extends NamedChannelsInput> - Class in org.anchoranalysis.plugin.mpp.experiment.bean
Converts NamedChannelsInput to a variety of others to match a delegate task
ConvertNamedChannels() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
ConvertNamedChannelsToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
Manager that converts (one channel) NamedChannelsInput to StackSequenceInput
ConvertNamedChannelsToStack() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
 
ConvertRGBToHSV - Class in org.anchoranalysis.plugin.opencv.bean.stack.provider.color
 
ConvertRGBToHSV() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToHSV
 
ConvertRGBToLab - Class in org.anchoranalysis.plugin.opencv.bean.stack.provider.color
 
ConvertRGBToLab() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToLab
 
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo
Converts a slice of single-channel into a newly created VoxelBuffer.
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
 
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
 
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
 
convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
 
ConvertTo<T> - Class in org.anchoranalysis.io.bioformats.copyconvert
Converts a subset of raw voxel bytes in a ByteBuffer to one or more destination channels.
ConvertTo(Function<VoxelsWrapper, Voxels<T>>) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo
 
convertTo3d(Point2d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
convertTo3i(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
convertTo3i(Point2i, int) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
ConvertToFactory - Class in org.anchoranalysis.io.bioformats.copyconvert
 
ConvertToImagePlus - Class in org.anchoranalysis.io.imagej.convert
Converts a channel or voxels into a ImagePlus.
ConvertToImageProcessor - Class in org.anchoranalysis.io.imagej.convert
Converts other voxel data-structures (as used by Anchor) to an ImageJ ImageProcessor.
ConvertToImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
Converts the Voxels and VoxelBuffer data-types used in Anchor to the Img used in ImgLib2.
ConvertToMat - Class in org.anchoranalysis.plugin.opencv.convert
Converts common image data-structures used by Anchor to the Mat class used by OpenCV.
ConvertToNativeImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
Converts the Voxels and VoxelBuffer data-types used in Anchor to the NativeImg used in ImgLib2.
convertToObjects(Dimensions) - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks
Creates an object-collection that is a voxelized representation of the marks in the annotation.
convertToOutputType(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
 
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertFromPhysicalVolume
 
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalAreaXY
 
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
 
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalVolume
 
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
 
ConvertToPhysicalAreaXY<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
 
ConvertToPhysicalAreaXY() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalAreaXY
 
ConvertToPhysicalDistance<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
 
ConvertToPhysicalDistance() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
 
ConvertToPhysicalDistance(Feature<T>, SpatialUnits.UnitSuffix, DirectionVector) - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
 
ConvertToPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
converts a feature to a physical distance in a XY place that is isometric
ConvertToPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalVolume
 
convertToUnits(double, String) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
Converts a value in base-units to another unit-type.
convertToUnits(double, SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
Converts a value in base-units to another unit-type.
ConvertToVoxelBuffer - Class in org.anchoranalysis.io.imagej.convert
Converts a ImageProcessor to a voxel-buffer of particular data-type.
ConvertUnits<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.physical
 
ConvertUnits() - Constructor for class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
 
convertUnsignedByte(UnsignedByteBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
 
convertUnsignedByte(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByte
 
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
 
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
 
convertUnsignedByte(UnsignedByteBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Copies a value from the current position in a UnsignedByteBuffer to the current position in a buffer of type T.
convertUnsignedInt(UnsignedIntBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
 
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
 
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
 
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
 
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
 
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
 
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
 
convertUnsignedInt(UnsignedIntBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Copies a value from the current position in a UnsignedIntBuffer to the current position in a buffer of type T.
convertUnsignedShort(UnsignedShortBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
 
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
 
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
 
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
 
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
 
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
 
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
 
convertUnsignedShort(UnsignedShortBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Copies a value from the current position in a UnsignedShortBuffer to the current position in a buffer of type T.
convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
 
convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromSignedShort
 
convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromUnsignedShort
 
ConvertWithHistogram - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
Converts a channel to a different voxel data-type by applying a converter with an associated histogram.
ConvertWithHistogram() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
 
convexHull2D(List<Point2i>) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
Like ConvexHullUtilities.convexHull2D(List, int) but uses a default minimum number of points.
convexHull2D(List<Point2i>, int) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
Apply a convex-hull algorithm to filter a set of points.
ConvexHull2D - Class in org.anchoranalysis.plugin.points.bean.mask.provider
Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
ConvexHull2D() - Constructor for class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull2D
 
ConvexHull3D - Class in org.anchoranalysis.plugin.points.bean.mask.provider
 
ConvexHull3D() - Constructor for class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull3D
 
ConvexHullBase - Class in org.anchoranalysis.plugin.points.bean.mask.provider
 
ConvexHullBase() - Constructor for class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
 
ConvexHullUtilities - Class in org.anchoranalysis.plugin.points.convexhull
 
copyAllChannels(Dimensions, ByteBuffer, DestinationChannelForIndex, int, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo
Copies the channels in the source buffer into a particular DestinationChannelForIndex.
copyAllFrames(IFormatReader, List<Channel>, ProgressReporter, ImageFileShape, ConvertTo<?>, ReadOptions) - Static method in class org.anchoranalysis.io.bioformats.copyconvert.CopyConvert
Copies all frames, channels, z-slices (in a byte-array) into a destination set of Channels converting them if necessary along the way
copyBufferIndexTo(T, int, T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
copyChange(MarkCollection) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
Makes a copy, with different marks
copyChangeIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
Copies the bean setting an new value for iterationsDilation
copyChangeParams(KeyValueParams) - Method in class org.anchoranalysis.feature.energy.EnergyStack
 
CopyConvert - Class in org.anchoranalysis.io.bioformats.copyconvert
Copies the bytes from a IFormatReader to a list of channels, converting if necessary.
CopyFilesExperiment - Class in org.anchoranalysis.plugin.io.bean.experiment
 
CopyFilesExperiment() - Constructor for class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
CopyFilesMethod - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
 
CopyFilesMethod() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CopyFilesMethod
 
CopyFilesNaming - Interface in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
 
CopyFilesNamingOne - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
 
CopyFilesNamingOne() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
 
CopyFilesNamingOneRegEx - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
 
CopyFilesNamingOneRegEx() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
 
copyFrom(int, int, ResultsVector, int) - Method in class org.anchoranalysis.feature.results.ResultsVector
Copies a contiguous subset of results from another vector
copyFrom(VoxelsWrapper, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Copies voxels from a source (of any type) to voxels of type T.
copyFromFloat(Voxels<FloatBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Copies voxels from a source of type @{link FloatBuffer} to voxels of type T.
copyFromUnsignedByte(Voxels<UnsignedByteBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.
copyFromUnsignedInt(Voxels<UnsignedIntBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T.
copyFromUnsignedShort(Voxels<UnsignedShortBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T.
copyInit(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine
Copies objects of a particular class from the define AND initializes
copyObjectsFrom(NamedProvider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
copyPixelsTo(int, BoundingBox, Voxels<UnsignedByteBuffer>, BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
Copies pixels on a particular channel to an output buffer
copyProvider(Class<?>, NamedProviderStore<T>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine
Copies objects of a particular class from the define AND initializes as a provider
copyStackCollectionFrom(NamedProvider<Stack>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
copyTo(NameValueSet<Feature<T>>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
copyToDirectory(File) - Method in class org.anchoranalysis.test.TestLoader
Copies all the data in the test-data folder (recursively), preserving file-dates
copyToDirectory(String[], File) - Method in class org.anchoranalysis.test.TestLoader
Copies specific subdirectories from the test-data folder (recursively), preserving file-dates
copyToDuplicate(NameValueSet<Feature<T>>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
copyVoxelsTo(ObjectMask, VoxelsWrapper, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
copyVoxelsTo(BoundingBox, VoxelsWrapper, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
copyWithoutInit(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine
Copies objects of a particular class from the define WITHOUT doing any initialization
cornerMin() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
 
cornerMin() - Method in class org.anchoranalysis.spatial.box.BoundingBox
The bottom-left corner of the bounding box.
CostMatrix<T> - Class in org.anchoranalysis.annotation.io.assignment
Stores costs between all possible pairings between elements from two lists.
CostOverlapWithinMidpointDistance - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
CostOverlapWithinMidpointDistance() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
 
count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
 
count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
 
count() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
Counts the number of values satisfying the predicate - across all voxels.
Count - Class in org.anchoranalysis.feature.bean.results
The number of the results from a particular feature.
Count - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Counts the number of items in a histogram (posssibly in relation to a threshold: above, below etc.)
Count() - Constructor for class org.anchoranalysis.feature.bean.results.Count
 
Count() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
 
countAtPosition(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernel
 
countAtPosition(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
This method is deliberately not broken into smaller pieces to avoid inlining.
countByte(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded
Counts all voxels in the intersection of two bounded-voxels of type BoundedVoxels that match a predicate.
countByteMasked(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded
Counts all voxels intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask and match a predicate.
CountEqual - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
 
CountEqual() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
 
Counter - Class in org.anchoranalysis.math.arithmetic
A simple counter that increments
Counter() - Constructor for class org.anchoranalysis.math.arithmetic.Counter
 
countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
 
countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
 
countForObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
Counts the number of values satisfying the predicate - but restricted to voxels corresponding to on in an object-mask.
countIntersectingVoxels() - Method in class org.anchoranalysis.mpp.overlap.MaxIntensityProjectionPair
 
countIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
countIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Counts the number of intersecting-voxels between two object-masks.
countIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects
Counts the number of intersecting-voxels between two object-masks.
CountKernel - Class in org.anchoranalysis.image.voxel.kernel.count
 
CountKernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernel
 
CountKernelNeighborhood - Class in org.anchoranalysis.image.voxel.kernel.count
For every voxel on the outline, count ALL neighbors that are adjacent, including those lying outside the scene.
CountKernelNeighborhood(boolean, BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
 
CountKernelNeighborhoodBase - Class in org.anchoranalysis.image.voxel.kernel.count
The number of touching-faces of a voxel with a neighbor
CountKernelNeighborhoodBase(boolean, BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
 
CountKernelNeighborhoodIgnoreOutsideScene - Class in org.anchoranalysis.image.voxel.kernel.count
For every voxel on the outline, count ALL neighbors that are adjacent, but ignoring any outside the scene.
CountKernelNeighborhoodIgnoreOutsideScene(boolean, BinaryValuesByte, boolean, Extent, ReadableTuple3i) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodIgnoreOutsideScene
 
CountKernelNeighborhoodMask - Class in org.anchoranalysis.image.voxel.kernel.count
The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an object-mask
CountKernelNeighborhoodMask(boolean, BinaryValuesByte, ObjectMask, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
 
countOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
countOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
countThreshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
 
countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
 
countThreshold(RelationToValue, double) - Method in class org.anchoranalysis.math.histogram.Histogram
 
CountVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
Like IterateVoxelsBoundingBox but counts voxels matching a predicate rather than iterating.
CountVoxelsIntersectingObjects - Class in org.anchoranalysis.image.voxel.iterator.intersecting
Like CountVoxelsIntersectingBounded but specifically counts areas of intersection between two ObjectMasks.
CoupledManifests - Class in org.anchoranalysis.plugin.io.manifest
 
CoupledManifests(Manifest, DeserializedManifest, Logger) - Constructor for class org.anchoranalysis.plugin.io.manifest.CoupledManifests
 
CoupledManifests(DeserializedManifest, int, Logger) - Constructor for class org.anchoranalysis.plugin.io.manifest.CoupledManifests
 
CoupledManifestsInputManager - Class in org.anchoranalysis.plugin.io.bean.input.manifest
 
CoupledManifestsInputManager() - Constructor for class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
create() - Method in interface org.anchoranalysis.bean.provider.Provider
 
create() - Method in class org.anchoranalysis.bean.provider.ProviderHolder
 
create() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProvider
 
create() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
 
create() - Method in class org.anchoranalysis.bean.shared.random.RandomNumberGeneratorBean
 
create() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
 
create() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
 
create() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
 
create() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
 
create() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
 
create() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
 
create() - Method in class org.anchoranalysis.bean.shared.StringMap
 
create() - Method in class org.anchoranalysis.feature.bean.list.Define
 
create() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
 
create() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
 
create() - Method in class org.anchoranalysis.feature.bean.list.FeatureListProvider
 
create() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
 
create() - Method in class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
 
create() - Method in class org.anchoranalysis.feature.bean.list.PrependName
 
create() - Method in class org.anchoranalysis.feature.bean.list.SelectFromShared
 
create() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProvider
 
create() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
 
create() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
 
create() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
 
create() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
 
create() - Method in class org.anchoranalysis.image.bean.interpolator.InterpolatorBean
 
create() - Method in class org.anchoranalysis.image.bean.interpolator.None
 
create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProvider
 
create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
 
create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
 
create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
 
create() - Method in class org.anchoranalysis.image.bean.provider.ColorProvider
 
create() - Method in class org.anchoranalysis.image.bean.provider.DimensionsProvider
 
create() - Method in class org.anchoranalysis.image.bean.provider.HistogramProvider
 
create() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
 
create() - Method in class org.anchoranalysis.image.bean.provider.MaskProvider
 
create() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
 
create() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProvider
 
create() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
 
create() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
 
create() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProvider
 
create() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
 
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
 
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
 
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory
 
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
 
create() - Method in class org.anchoranalysis.mpp.bean.provider.MarkBoundsProvider
 
create() - Method in class org.anchoranalysis.mpp.bean.provider.MarkCollectionProvider
 
create() - Method in class org.anchoranalysis.mpp.bean.provider.SingleMarkProvider
 
create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator
 
create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
 
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
 
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
 
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
 
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
 
create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
create() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
 
create() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
 
create() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
 
create() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions
 
create() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
 
create() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
 
create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
 
create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
 
create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
 
create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Empty
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
 
create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
 
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
 
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
 
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
 
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
 
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
 
create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
 
create() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
 
create() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
 
create() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
 
create() - Method in interface org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder.CreateFirstSecondOrder
 
create() - Method in class org.anchoranalysis.plugin.imagej.bean.interpolator.InterpolatorBeanImageJ
 
create() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
 
create() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
 
create() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
 
create() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
 
create() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
create() - Method in class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory
Creates a RotationMatrix.
create() - Static method in class org.anchoranalysis.test.feature.ConstantsInListFixture
creates a feature-list associated with the fixture
create(boolean) - Method in interface org.anchoranalysis.core.concurrency.ConcurrentModelPool.CreateModelForPool
Creates a model
create(boolean, Supplier<T>) - Static method in class org.anchoranalysis.bean.OptionalFactory
Creates only if a boolean flag is true, otherwise returns empty.
create(int) - Method in class org.anchoranalysis.image.core.object.label.DecodeLabels
Creates a list of elements from voxels that are labelled with unique integers (sequentially increasing)
create(int) - Method in interface org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactory
 
create(int) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactoryHistogramReuse
 
create(int) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitonFactoryHistogram
 
create(BufferedImage) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.CreateStackFromBufferedImage
 
create(Class<? extends FeatureInput>) - Method in interface org.anchoranalysis.feature.calculate.cache.CacheCreator
 
create(Class<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.session.cache.creator.CacheCreatorSimple
 
create(String) - Static method in class org.anchoranalysis.bean.OptionalFactory
Creates Optional.empty() for an empty string, or otherwise Optional.of
create(String) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Creates an Optional from a string that might be empty or null
create(String, Optional<ManifestDescription>, OutputterChecked, String) - Static method in class org.anchoranalysis.io.generator.text.TextFileOutputter
Creates a TextFileOutput.
create(Path) - Static method in class org.anchoranalysis.io.generator.tabular.CSVWriter
Creates and starts a CSVWriter (it's always allowed, so will never return null)
create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.bean.Plot
Creates a graph
create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.LinePlot
 
create(List<Point3d>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
 
create(List<Point3d>, int) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
 
create(List<Point3i>) - Static method in class org.anchoranalysis.image.core.object.factory.SingleObjectFromPointsFactory
 
create(List<T>) - Method in interface org.anchoranalysis.bean.xml.factory.CreateFromList
 
create(List<T>, List<T>, boolean, CheckedToDoubleBiFunction<T, T, CreateException>) - Static method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
Creates by calculating the cost between elements.
create(List<V>, Function<V, ObjectMask>, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph
Create the graph with object-masks as vertices, where edges represent the number of intersecting voxels between objects.
create(Map<Integer, T>, UnaryOperator<T>) - Method in class org.anchoranalysis.image.core.object.label.DecodeLabels
Creates a map of elements to other elements that are labelled with unique integers (sequentially increasing) in voxels.
create(Optional<String>, String) - Static method in class org.anchoranalysis.feature.io.name.MultiNameFactory
Creates either a multi-name that is either has a single part or a double part.
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
 
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
 
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules
Creates rules for determining whether an output is enabled or disabled.
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.Permissive
 
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
 
create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
 
create(IFormatReader, VoxelDataType, int) - Static method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertToFactory
 
create(Provider<T>) - Static method in class org.anchoranalysis.bean.OptionalFactory
Creates from a provider if non-null.
create(SharedObjects) - Static method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsInitParams
 
create(SharedObjects) - Static method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
 
create(Logger, Path) - Static method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
Creates empty params
create(FeatureList<T>, SharedFeatureSet<T>) - Method in interface org.anchoranalysis.feature.session.cache.FeatureSessionCacheFactory
 
create(FeatureList<T>, SharedFeatureSet<T>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCacheFactory
 
create(FeatureList<T>, SharedFeatureSet<T>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCacheFactory
 
create(FeatureCSVMetadata, Outputter) - Static method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
Maybe creates a FeatureCSVWriter depending if the output is allowed.
create(ImageInitParams, SharedObjects) - Static method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
 
create(Channel) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
 
create(Channel) - Static method in class org.anchoranalysis.image.core.stack.DisplayStack
 
create(Channel, Mask) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
 
create(Channel, ObjectCollection) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
 
create(Channel, ObjectMask) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
 
create(Dimensions, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
Creates an empty initialized channel for a particular data-type
create(RGBStack) - Static method in class org.anchoranalysis.image.core.stack.DisplayStack
 
create(Stack) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageFactory
 
create(Stack) - Static method in class org.anchoranalysis.image.core.stack.DisplayStack
 
create(BinaryVoxels<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
 
create(VoxelBuffer<?>) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory
 
create(SliceBufferIndex<T>) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
 
create(SliceBufferIndex<T>, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
 
create(ObjectCollection, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph
Create the graph with object-masks as vertices, where edges represent the number of intersecting voxels between objects.
create(Voxels<?>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
 
create(Voxels<?>, Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
 
create(Voxels<?>, Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
 
create(VoxelsWrapper) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory
 
create(VoxelsWrapper, Optional<ObjectMask>) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
 
create(InputManagerParams) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
 
create(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Combine
 
create(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
 
create(InputManagerParams) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
 
create(InputOutputContext, Optional<Define>, Optional<? extends InputForMPPBean>) - Static method in class org.anchoranalysis.mpp.io.input.MPPInitParamsFactory
 
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination
Creates a logger for this destination
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
 
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
 
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToConsole
 
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple
 
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFile
 
create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileOnlyIfFailure
 
create(Mark) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
create(Mark, EnergyStackWithoutParams, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.memo.PxlMarkMemoFactory
 
create(Mark, EnergyStackWithoutParams, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.VoxelizedMarkFactory
 
create(Extent, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
 
create(CommandLine, Path, Path, Path) - Static method in class org.anchoranalysis.launcher.executor.ExperimentExecutorFactory
Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR accepts a path passed as the first command-line argument
createAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
 
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
 
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
 
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
 
createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
 
createAndStartSession() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
 
createArguments(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
 
createAscending() - Static method in class org.anchoranalysis.test.feature.plugins.HistogramFixture
a histogram from 0 to 255 (inclusive) where each bin is equal to its index (value 5 has count 5, value 100 has count 100 etc.)
createAssignment(ObjectCollection, ObjectCollection, double, Dimensions) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentObjectFactory
 
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
 
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
 
createAsStack() - Method in class org.anchoranalysis.image.bean.provider.ChannelProvider
 
createAsStack() - Method in class org.anchoranalysis.image.bean.provider.MaskProvider
 
createAsStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProvider
 
createAsStack() - Method in interface org.anchoranalysis.image.core.stack.ProviderAsStack
Creates from the image-bean in the form of a stack
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
 
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
 
createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
 
createBackground(NamedProviderStore<Stack>, String) - Static method in class org.anchoranalysis.mpp.io.output.BackgroundCreator
 
createBean(Class<?>, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
 
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.define.DefineFactory
 
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IncludeBeanFactory
 
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IncludeListFactory
 
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IndirectlyFromListBeanFactory
 
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.ListBeanFactory
 
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.ReplacePropertyBeanFactory
 
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.StringListFactory
 
createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.StringSetFactory
 
createBeanInstance(Class<?>, BeanDeclaration) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
 
createBetweenTwoPoints(Point3d, Point3d) - Static method in class org.anchoranalysis.image.core.orientation.DirectionVector
 
createBetweenTwoPoints(Point3i, Point3i) - Static method in class org.anchoranalysis.image.core.orientation.DirectionVector
 
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in interface org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStack
 
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
 
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Single
 
createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
createBufferedImage() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
createBufferedImage(int, int) - Method in class org.anchoranalysis.plot.PlotInstance
 
createBufferedImageBBox(BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
createByte() - Method in class org.anchoranalysis.image.core.mask.Mask
 
createByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
 
createByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
Create voxels-extracter for UnsignedByteBuffer.
createByte(Voxels<UnsignedByteBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
Create voxels-assigner for UnsignedByteBuffer.
createByte(BoundingBox) - Static method in class org.anchoranalysis.image.voxel.BoundedVoxelsFactory
 
createByte(Extent, IntFunction<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory
Create voxels-arithmethic for UnsignedByteBuffer
createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
 
createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
 
createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
 
createCalculator(CreateCalculatorHelper, ImageInitParams, BoundReplaceStrategy<FeatureInputStack, ? extends ReplaceStrategy<FeatureInputStack>>) - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
 
createChannel() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
 
createChannel(int, boolean) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
createChannelDuplicate(int) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
createChannelDuplicateForBoundingBox(int, BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
createChart(DefaultCategoryDataset, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.BarPlot
Creates a chart
createChart(DefaultBoxAndWhiskerCategoryDataset, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.BoxPlot
 
createChart(XYDataset, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.LinePlot
Creates a chart
createChart(S, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
createCollection(Channel, ObjectCollection, CalculateLevel, int, MessageLogger) - Static method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollectionFactory
 
createColor(ColoredMarks, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
 
createColors(int) - Method in class org.anchoranalysis.annotation.io.assignment.generator.ColorPool
 
createCombinedContour() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
 
createCombinedException(String, Throwable) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
 
CreateCombinedStack - Class in org.anchoranalysis.image.bean.nonbean.init
 
createConnectedComponents(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
 
createConverter() - Method in class org.anchoranalysis.image.bean.channel.converter.ConvertChannelTo
 
createConverter() - Method in class org.anchoranalysis.image.bean.channel.converter.ConvertChannelToWithHistogram
 
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
 
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
 
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
 
createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
 
createCountKernelMask(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
 
createDataset(Iterator<T>) - Method in class org.anchoranalysis.plot.index.LinePlot
 
createDataset(Iterator<T>) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
createDataset(Iterator<T>) - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
Creates a sample dataset
createDefaultDataset() - Method in class org.anchoranalysis.plot.index.BarPlot
 
createDefaultDataset() - Method in class org.anchoranalysis.plot.index.BoxPlot
 
createDefaultDataset() - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
 
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
 
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
 
createDescending() - Static method in class org.anchoranalysis.test.feature.plugins.HistogramFixture
 
createDescriptor(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
 
createDesignMatrix(List<Point3f>) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
 
createDestinationFile(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CopyFilesMethod
 
createDilatedObject(ObjectMask, Optional<Extent>, boolean, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation
Dilates an object-mask, growing the bounding-box as necessary.
createDilationKernel(BinaryValuesByte, Optional<Voxels<UnsignedByteBuffer>>, int) - Method in class org.anchoranalysis.image.voxel.object.morphological.DilationKernelFactory
 
createDim() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
createDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
 
createDims() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
Returns the dimensions or null if none are provided
createDistanceMapForMask(Mask, boolean, double, double, boolean, boolean) - Static method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>, boolean, double, double, boolean, boolean) - Static method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
createDocumentBuilder() - Static method in class org.anchoranalysis.bean.xml.XmlUtilities
 
createDuplicatePxlMarkMemoList() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
CreateEllipse - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
 
CreateEllipse() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
 
createEmptyInitialised(Dimensions) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
 
createEmptyInitialisedToSupportMaxValue(Dimensions, long) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
Creates an empty initialized channel with discrete type with as minimal as needed data-type to support a maximum value
createEmptyMat(Extent, int) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
 
createEmptyOff(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off (0).
createEmptyOff(Extent, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
Creates an empty binary-voxels of a particular data-type with all voxels initialized to OFF (0)
createEmptyOn(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to ON (255)
createEmptyUninitialised(Dimensions) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
 
createEnergyStack(ImageInitParams, Logger) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
 
createErodedObject(ObjectMask, Optional<Extent>, boolean, int, boolean, Optional<AcceptIterationConditon>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion
 
CreateException - Exception in org.anchoranalysis.core.exception
 
CreateException(String) - Constructor for exception org.anchoranalysis.core.exception.CreateException
 
CreateException(String, AnchorCombinableException) - Constructor for exception org.anchoranalysis.core.exception.CreateException
 
CreateException(String, HasFriendlyErrorMessage) - Constructor for exception org.anchoranalysis.core.exception.CreateException
 
CreateException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.CreateException
 
createExperimentExecutor(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
 
createExperimentOutputter(String, Manifest, RecordedOutputsWithRules, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.OutputManager
Creates an outputter for the experiment in general.
createExperimentState() - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
 
createExperimentState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
 
createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueIndividualEnergyGreaterThan
 
createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueMarkGreaterEqualThan
 
CreateFeatureInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session
 
createFeatureList(String, TestLoader) - Static method in class org.anchoranalysis.test.feature.plugins.FeaturesFromXmlFixture
 
createFeatureNames() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
createFeatureNames() - Method in interface org.anchoranalysis.image.feature.session.FeatureTableCalculator
Creates A list of names for each feature (columns of the table)
createFeatureNames() - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
createFeatureNames() - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
 
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
Creates features that will be applied on the objects.
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
 
createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
 
createFeatures(NamedFeatureStore<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
 
createFeatureSession() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
Creates session for evaluating feature optionally adding an energy-stack.
createFeatureSession(UnaryOperator<FeatureList<T>>, SharedObjects) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
Creates session for evaluating features.
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
 
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
 
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in interface org.anchoranalysis.io.output.writer.Writer
The path to write a particular output to.
createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors
The path to write a particular output to.
createFileOutputFor(String, FeedbackBeginParameters<VoxelizedMarksWithEnergy>, String) - Static method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterUtilities
 
createFitResultFromMatrixAandCenter(DoubleMatrix2D, DoubleMatrix2D, boolean) - Static method in class org.anchoranalysis.plugin.points.bean.fitter.EllipsoidFitHelper
 
createFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
Create voxels-extracter for FloatBuffer
createFloat(Voxels<FloatBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
Create voxels-assigner for FloatBuffer.
createFloat(Extent, IntFunction<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory
Create voxels-arithmethic for FloatBuffer
createForBuffer(VoxelBuffer<T>, Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
 
createForDirectoryPermissive(Path, boolean) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked
Creates, defaulting to a permissive output-manager in a a particular directory.
createForFeature(Feature<?>) - Method in interface org.anchoranalysis.feature.session.CreateFeatureInput
 
createForFeatures(List<NamedBean<FeatureListProvider<T>>>, LabelHeaders, ResultsWriterOutputNames, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
Alternative static constructor that creates a shared-state from a list of named feature-providers
createForFeatures(ResultsWriterOutputNames, FeatureTableCalculator<T>, LabelHeaders, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
Alternative static constructor that creates a shared-state from a feature-store
createForFeatures(NamedFeatureStore<T>, LabelHeaders, ResultsWriterOutputNames, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
Alternative static constructor that creates a shared-state from a feature-store
createForSingle(AnchorBean<?>, String) - Static method in class org.anchoranalysis.bean.permute.setter.PermutationSetterUtilities
Searches through a list of property fields to find one that matches the propertyName
createForSubdirectory(String) - Method in class org.anchoranalysis.test.TestLoader
Creates a new test-loader for a subdirectory of the current test
createFrom(int, ObjectMask) - Method in interface org.anchoranalysis.image.core.object.label.DecodeLabels.CreateElementFromScaledObject
 
createFrom(int, ObjectMask) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
Creates an element of type T from an object-representation and index.
createFrom3Vecs(DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D) - Static method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
createFromChannel(Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D
 
createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
 
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
 
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.MeanFilter2D
 
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.VarianceFilter2D
 
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter2D
 
createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
 
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
 
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
 
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
 
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
 
createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
 
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
 
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
 
createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
 
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
 
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
 
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
 
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
 
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
 
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOff
 
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOn
 
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
 
createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
 
createFromExistingCollections(InputOutputContext, Optional<Define>, Optional<NamedProvider<Stack>>, Optional<NamedProvider<ObjectCollection>>, Optional<KeyValueParams>) - Static method in class org.anchoranalysis.mpp.io.input.MPPInitParamsFactory
 
createFromExplicitDirectory(String) - Static method in class org.anchoranalysis.test.TestLoader
Creates a new test-data loader using an explicit File path as root
createFromExplicitDirectory(Path) - Static method in class org.anchoranalysis.test.TestLoader
Creates a new test-data loader using an explicit File path as root
createFromFile(Path) - Method in class org.anchoranalysis.io.manifest.directory.sequenced.DeriveElementsFromSequencedDirectory
Creates an element of type T from a one particular file in the sequence.
createFromFile(Path) - Method in class org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectoryDeserializer
 
createFromFlag(boolean, Supplier<T>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Creates an Optional from a boolean flag
createFromFlag(boolean, T) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Creates an Optional from a boolean flag
createFromFlagChecked(boolean, CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Creates an Optional from a boolean flag - where the supplier can thrown an exception
createFromFlagOptional(boolean, Supplier<Optional<T>>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Creates an Optional from a boolean flag and a supplier that returns an Optional
createFromHistogram(Histogram) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
 
createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
 
createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
 
createFromList(List<T>, Function<T, BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundedList
Creates for a list, minimally fitting a bounding-box around all elements
CreateFromList<T> - Interface in org.anchoranalysis.bean.xml.factory
 
createFromMarks(MarkCollection, KernelCalculationContext, Logger) - Static method in class org.anchoranalysis.plugin.mpp.segment.optimization.VoxelizedMarksWithEnergyFactory
 
createFromMask(Mask) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
 
createFromMask(Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
 
createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull2D
 
createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull3D
 
createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
 
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
 
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
 
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
 
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
 
createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
 
createFromMavenWorkingDirectory() - Static method in class org.anchoranalysis.test.TestLoader
Creates a new test-data loader finding "src/test/resources" using the Maven working directory
createFromMavenWorkingDirectory(String) - Static method in class org.anchoranalysis.test.TestLoader
Creates a new test-data loader finding "src/test/resources/PLUS_SOMETHING" using the Maven working directory
createFromNotObjects(ObjectCollection, Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFromObjects
We look for space NOT in the objects, and create channel to display it
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
 
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
 
createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
 
createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
 
createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
 
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
 
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
 
createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
 
createFromObjects(ObjectCollection, Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFromObjects
We look for space IN objects, and create channel to display it
createFromOutputter(String, OutputterChecked) - Static method in class org.anchoranalysis.io.generator.tabular.CSVWriter
Creates and starts a CSVWriter if it's allowed, otherwise returns Optional.empty().
createFromOverlays(ColoredOverlayCollection, IdentifierGetter<Overlay>, IdentifierGetter<ObjectWithProperties>) - Static method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributesFactory
 
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
 
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
 
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
 
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
 
createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
 
createFromStack(Stack) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
 
createFromStack(Stack) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
 
createFromStack(Stack) - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ColorConverterBase
 
createFromString(String) - Static method in class org.anchoranalysis.spatial.axis.AxisTypeConverter
Maps a string of x, y, z (case ignored) to a corresponding axis type
createFromTupleDuplicate(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.Extent
Createss an extent from a point (duplicating the point for internal use)
createFromTupleReuse(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.Extent
Creates from a point that is reused internally (without duplication)
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
 
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
Creates masks from some combination of two masks
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
 
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
 
createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor
 
createGrayscaleByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageFactory
 
createGroupMap(ConsistentChannelChecker) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
Creates a map for the storing an aggregate-data-object for each group.
createGroupMap(ConsistentChannelChecker) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
 
createGroupMap(ConsistentChannelChecker) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
 
createHashMapToId() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
createHeaders() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
createHeaders() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
 
createHeaders(boolean) - Method in class org.anchoranalysis.plugin.image.task.feature.GenerateLabelHeadersForCSV
Creates the label-headers (the headers for columns not associated with features)
createHistogramIgnoreZero(Channel, ObjectMask, boolean) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
 
createIdArr() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
createIdHashMap() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
createImageDim() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
 
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
 
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
 
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
 
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
 
createInitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
 
createInitParams(Optional<SharedObjects>, Optional<EnergyStack>) - Static method in class org.anchoranalysis.image.feature.session.InitParamsHelper
 
createInitParams(InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
 
createInitParams(InputOutputContext, Optional<NamedProvider<Stack>>, Optional<NamedProvider<ObjectCollection>>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
 
createInitParams(InputForMPPBean, InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
 
createInputContext() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
Creates an input-context, reusing parameters from the experiment-execution
createInputProcessContext(Optional<String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
 
createInputProcessContext(Optional<String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
 
createInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
 
createInt(Voxels<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
Create voxels-extracter for UnsignedIntBuffer
createInt(Voxels<UnsignedIntBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
Create voxels-assigner for UnsignedIntBuffer.
createInt(BoundingBox) - Static method in class org.anchoranalysis.image.voxel.BoundedVoxelsFactory
 
createInt(Extent, IntFunction<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory
Create voxels-arithmethic for UnsignedIntBuffer
createIntersectionComplement(ColoredOverlayCollection, ColoredOverlayCollection) - Static method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
createInverted() - Method in class org.anchoranalysis.image.core.mask.Mask
 
createInverted() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
Inverts the values so OFF becomes ON, and vice-versa
createKernelFactoryNames() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
createKeyValueParams() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
returns the associated KeyValueParams or an empty set, if no params are associated with the energyScheme
createLabelledChannel(BoundedList<T>, Optional<Map<Integer, T>>) - Method in class org.anchoranalysis.image.core.object.label.LabelObjects
Creates a channel that contains a unique integer (label) for each element's object-representation.
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorScheme
Creates a list of colors of particular size.
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
 
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList
 
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle
 
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.HSB
 
createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.VeryBright
 
createListChildFeatures() - Method in class org.anchoranalysis.feature.bean.Feature
Returns a list of Features that exist as bean-properties of this feature, either directly or in lists.
createListMembershipWithFlags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
createManifestDescription() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
 
createManifestDescription() - Method in class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
 
createManifestDescription() - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator
 
createManifestDescription() - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
 
createManifestDescription() - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
 
createManifestDescription() - Method in class org.anchoranalysis.io.generator.tabular.CSVGenerator
 
createManifestDescription() - Method in class org.anchoranalysis.io.generator.text.StringGenerator
 
createManifestDescription() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
 
createManifestDescription() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
 
createManifestDescription(String) - Static method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
 
createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.Autoname
 
createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
 
createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
 
createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
 
createMapToIndex() - Method in class org.anchoranalysis.feature.name.FeatureNameList
Creates a map from the feature-names to their indices in the list
createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>, CreateException>, Dimensions, boolean, double) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.EllipsoidFactory
 
createMarkEllipsoidLeastSquares(ObjectMask, Dimensions, boolean, double) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.EllipsoidFactory
Creates a MarkEllipsoid using least-squares fitting to the points on the outline of an object-mask
createMarkFromPoint(Point3d, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory
 
createMarkFromPoint(Point3i, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory
 
CreateMarkFromPoints - Class in org.anchoranalysis.mpp.bean.points
 
CreateMarkFromPoints() - Constructor for class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
 
createMarkFromPoints3f(List<Point3f>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
 
createMarkFromPoints3i(List<Point3i>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
 
createMaskOff(Dimensions) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory
Creates a binary-mask for specific dimensions with all voxels set to OFF
createMaskOff(Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory
Creates a binary-mask for specific dimensions with all voxels set to OFF
createMaskOn(Dimensions) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory
Creates a binary-mask for specific dimensions with all voxels set to ON
createMaskOn(Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory
Creates a binary-mask for specific dimensions with all voxels set to ON
createMerged(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
createMerged(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
createMerged(OverlayCollection) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
createMessageForDscr(String) - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
 
createMessageForDscr(String) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
 
createMessageForDscr(String) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
Creates a message for the exception from the description
createMessageForDscr(String) - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
 
createMinusOne() - Method in class org.anchoranalysis.spatial.Extent
Creates a new Extent with each dimension decreased by one
createMockFeatureWithCalculation() - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture
Creates a mock-feature (using a mock-FeatureCalculation under the hood) which counts the number of pixels in an object
createMockFeatureWithCalculation(ToDoubleFunction<T>) - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture
Creates a mock-feature (using a mock-FeatureCalculation under the hood) with a result calculated using a lambda
createModelPool(ConcurrencyPlan) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled
Creates the model pool (to be used by multiple threads)
createModelPool(ConcurrencyPlan) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
 
createModelPool(ConcurrencyPlan) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
 
createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStoreFactory
Create a list of na
createNamedFeatureProviders(String, TestLoader) - Static method in class org.anchoranalysis.test.feature.plugins.FeaturesFromXmlFixture
 
createNames() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
createNecessaryDirectories(Path) - Static method in class org.anchoranalysis.annotation.io.WriterUtilities
 
CreateNew - Class in org.anchoranalysis.plugin.image.bean.channel.provider
Creates a new channel with all values initialized to a constant (by default zero)
CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
 
CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
Creates a new empty collection of marks
CreateNew() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
 
CreateNew() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.CreateNew
 
CreateNew() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew
 
createNewMarkPos(Orientation2D, Ellipse, RandomNumberGenerator, Dimensions, double, double, boolean) - Static method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
createNext(int, int) - Method in interface org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement.TableCreator
 
createNullErrorReporter() - Static method in class org.anchoranalysis.core.log.LogUtilities
 
createObject(Mask) - Static method in class org.anchoranalysis.image.core.object.factory.SingleObjectFromChannelFactory
 
createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
 
createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
 
createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.Overlay
 
createObjects() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.Comparer
 
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
 
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
 
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
 
createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
 
createOneToMany(Generator<T>, CheckedFunction<S, Stream<T>, ?>) - Static method in class org.anchoranalysis.io.generator.GeneratorBridge
Creates a bridge that maps ONE-TO-MANY from source to destination (i.e.
createOneToOne(Generator<T>, CheckedFunction<S, T, ?>) - Static method in class org.anchoranalysis.io.generator.GeneratorBridge
Creates a bridge that maps ONE-TO-ONE from source to destination (i.e.
createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
 
createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
 
createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
 
createOrReuse(Throwable) - Static method in exception org.anchoranalysis.core.exception.InitException
 
createOrReuse(T) - Method in class org.anchoranalysis.feature.session.strategy.replace.AlwaysNew
 
createOrReuse(T) - Method in class org.anchoranalysis.feature.session.strategy.replace.CacheAndReuseStrategy
 
createOrReuse(T) - Method in interface org.anchoranalysis.feature.session.strategy.replace.ReplaceStrategy
 
createOrReuse(T) - Method in class org.anchoranalysis.feature.session.strategy.replace.ReuseSingletonStrategy
 
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
 
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendFilePath
 
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
 
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
 
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendMarks
 
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendObjects
 
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
 
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
 
createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
createPair(CreateCalculatorHelper, ImageInitParams, CacheTransferSourceCollection) - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
 
createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
createParam(String, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
createParams(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelFaces
 
createParams(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
 
createParams(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
 
createParamsForImage(EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.KeyValueParamsForImageCreator
 
createPathDeriver(String, String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
Creates a (rooted) file-path generator for a rootName and a regEx which matches three groups The first group should correspond to top-level folder for the project The second group should correspond to the unique name of the dataset.
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
 
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
 
createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
Determines the payload for any given or potential vertex
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
 
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
 
createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
createPolicy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
 
createPrecalc(DrawOverlay, ObjectWithProperties, Dimensions) - Static method in class org.anchoranalysis.overlay.writer.DrawOverlay
 
createPrefixerContext() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
 
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
 
createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
Determines the priority (and selection criteria) used to allow merges between neighbors
createPriority(ObjectVertex, ObjectVertex, Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.priority.Prioritizer
 
CreateProposalVisualization - Interface in org.anchoranalysis.mpp.proposer.visualization
 
CreateProposeVisualizationList - Class in org.anchoranalysis.mpp.proposer.visualization
 
CreateProposeVisualizationList() - Constructor for class org.anchoranalysis.mpp.proposer.visualization.CreateProposeVisualizationList
 
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
 
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
 
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
createRasters(AnnotationWithMarks, DisplayStack, Path, ColorScheme, Path, Logger, boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
createReducedFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
 
createRGB(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageFactory
 
createRGBMaskGenerator(DrawObject, DisplayStack, ColorList) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
 
createRGBStack(Channel, Channel, Channel, VoxelDataType) - Static method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
createRoot() - Static method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
 
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.Orientation
 
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
createRow(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
 
createSameSize(ChannelProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
Creates a new channel from a provider, making sure it's the same size as an an existing channel
createSameSize(MaskProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
Creates a new channel from a provider, making sure it's the same size as an an existing channel
createScaledMask(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.scaled.FromMask
 
createScaledMask(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in interface org.anchoranalysis.overlay.object.scaled.ScaledMaskCreator
Creates a scaled-version of the mask
createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
 
createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
 
createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.Overlay
 
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
 
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
 
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
Creates a new second-level SingleLevelOutputEnabled from the relevant set of strings.
createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
 
createSequence(VoxelDataType) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
 
createSession() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
 
createSet() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
createSet() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
createSet() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty
 
createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
 
createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
 
createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<S>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
 
createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<U>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
 
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
Creates a shared-state for the duration of a particular input-job
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
Sets a new output-sequence for the series
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
createShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
Create voxels-extracter for UnsignedShortBuffer.
createShort(Voxels<UnsignedShortBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
Create voxels-assigner for UnsignedShortBuffer.
createShort(Extent, IntFunction<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory
Create voxels-arithmethic for UnsignedShortBuffer
createSingle(CreateCalculatorHelper, ImageInitParams, BoundReplaceStrategy<FeatureInputSingleObject, CacheAndReuseStrategy<FeatureInputSingleObject>>) - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
 
createSingle(T, Function<T, BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundedList
Creates for a single element, using its current bounding-box.
createStack(List<RGBStack>, ChannelFactorySingleType) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.RasterArranger
 
CreateStackFromBufferedImage - Class in org.anchoranalysis.image.core.stack.bufferedimage
 
createStackSequenceForSeries(int) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
 
createStatistics() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
 
createStatistics() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
 
createStatistics() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
createStatistics() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.mpp.bean.mark.MarkRegion
 
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
 
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
 
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
 
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.MaxNonZero
 
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
 
createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
 
createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
 
createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
 
createStatisticsHeaderNames() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
 
createStatisticsHeaderNames() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
 
createStatisticsHeaderNames() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
The headers needed to create statistics
createSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors
Maybe creates a subdirectory for writing to.
createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
 
createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
 
createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in interface org.anchoranalysis.io.output.writer.Writer
Maybe creates a subdirectory for writing to.
createSubset(IntPredicate) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
createSubset(List<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
A subset of the collection identified by particular indices.
createSubsetFromIDs(IntPredicate) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
createUninitialised(Dimensions, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
 
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
 
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
 
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
 
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
 
createUninitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
 
createUniqueNamesSorted() - Method in class org.anchoranalysis.feature.name.FeatureNameList
 
createValues() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
createValues() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
 
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
 
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean
Creates a vector in a particular direction
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
createVector3d() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
 
createWithConsoleFallback(OutputterChecked, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination
Creates a logger for this destination - and if anything goes wrong reporting fallback into the console.
createWithDir(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CompressTIFF
 
createWithDir(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CopyFilesMethod
 
createWithDir(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.SimpleCopy
 
createWithLogFallback(OutputterChecked, MessageLogger, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination
Creates a logger for this destination - and if anything goes wrong reporting fallback into a log.
createWithoutColor(ObjectCollection, IdentifierGetter<ObjectMask>) - Static method in class org.anchoranalysis.overlay.collection.OverlayCollectionObjectFactory
 
createWithoutColor(MarkCollection, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
 
createWithPrefix(DirectoryWithPrefix, MultiLevelOutputEnabled, OutputWriteSettings, Optional<WriteOperationRecorder>, Optional<MultiLevelRecordedOutputs>, boolean) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked
Creates a bound output-manager from an existing OutputManager with a prefix.
createWithRangeLimits(Iterator<T>, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
Creates or gets an instance of IFormatWriter which dictates the file format to use for writing.
createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMETiff
 
createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMEXML
 
createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
 
cross(Vector3d, Vector3d) - Static method in class org.anchoranalysis.spatial.point.Vector3d
 
CSVGenerator<T> - Class in org.anchoranalysis.io.generator.tabular
 
CSVGenerator(String) - Constructor for class org.anchoranalysis.io.generator.tabular.CSVGenerator
 
CSVReporterAggregated - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
Outputs statistics on current energy / kernel acceptance etc.
CSVReporterAggregated() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
 
CSVReporterBest - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
Outputs a CSV with statistics on the configuration/energy only the best configuration state changes.
CSVReporterBest() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
 
CSVReporterUtilities - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
CSVRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
A row of the CSV File
CSVRow(ColumnDefinition) - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
 
csvString() - Method in class org.anchoranalysis.math.histogram.Histogram
 
CSVWriter - Class in org.anchoranalysis.io.generator.tabular
 
CUBIC_MICRO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
 
CUBIC_NANO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
 
currentStateDescription() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
currentTemperature() - Method in class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
 
currentTemperature() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
 
currentTemperature() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.NoAnnealing
 
customizeExperimentTemplate(ExperimentExecutor, CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
 
CustomManagerFromPath - Class in org.anchoranalysis.launcher.executor.selectparam.path
Loads a custom-manager from a path
CustomManagerFromPath(Path) - Constructor for class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
 
CutBelowThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold value
CutBelowThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
 
CVFindContours - Class in org.anchoranalysis.plugin.opencv
Wrapper around Open CV's findContours function
CVInit - Class in org.anchoranalysis.plugin.opencv
Provides for initialization of the JavaCPP bridge to OpenCV.

D

dataType() - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
 
dataType() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
Data-type of each voxel in the buffer.
dataType() - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
 
dataType() - Method in class org.anchoranalysis.image.voxel.Voxels
 
DataTypeMaxIntensity<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
The maximum-intensity allowed by the data-type of the stack (e.g.
DataTypeMaxIntensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
 
DebugDependentProcessor<T extends InputFromManager,​S> - Class in org.anchoranalysis.experiment.bean.processor
Executes different processors depending on whether we are in debug mode or not
DebugDependentProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
 
decode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
Decodes a chain-code into a point
decodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
DecodeLabels<T> - Class in org.anchoranalysis.image.core.object.label
Decodes a labelled raster into derived objects or object-like elements.
DecodeLabels(Voxels<?>, int, int, DecodeLabels.CreateElementFromScaledObject<T>) - Constructor for class org.anchoranalysis.image.core.object.label.DecodeLabels
 
DecodeLabels.CreateElementFromScaledObject<T> - Interface in org.anchoranalysis.image.core.object.label
Creates an element from the scaled-object and its index
DecomposeIntoConnectedComponents - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
Ensures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.
DecomposeIntoConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
 
decrement() - Method in class org.anchoranalysis.math.arithmetic.Counter
 
decrementX() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
decrementX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
decrementY() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
decrementY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
decrementZ() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
decrementZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
deepCopy() - Method in class org.anchoranalysis.core.color.ColorList
 
deepCopy() - Method in class org.anchoranalysis.feature.energy.EnergyTotal
 
deepCopy() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
deepCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
Make a deep copy (except the energyScheme which is reused).
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
Creates a deep-copy of the marks
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
 
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
deepCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
deepCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
deepCopy() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
deepCopy() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
Default - Class in org.anchoranalysis.io.bioformats.bean.options
 
Default() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.Default
 
DEFAULT_COLOR_SET_GENERATOR - Static variable in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
 
DEFAULT_FUNC_NUM_PIXELS - Static variable in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture
 
DEFAULT_IMAGE_INPUT_NAME - Static variable in class org.anchoranalysis.mpp.io.input.MultiInput
 
defaultColorIndexFor(int) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
 
defaultExperimentOrCustom(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.experiment.ExperimentFactory
Chooses either a path to the default-experiment or a path to a custom experiment.
DefaultFindChildStrategy - Class in org.anchoranalysis.feature.session.strategy.child
The default strategy for finding children by always directly taking (or creating a child-cache) as necessary.
DefaultInstance - Annotation Type in org.anchoranalysis.bean.annotation
Indicates a default bean-instance is available.
defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
 
defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.task.Task
If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
If specified, default rules for determine which outputs are enabled or not.
defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
 
defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
 
Define - Class in org.anchoranalysis.bean.define
A bean where the definitions of many different NamedBeans can be specified.
Define<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
 
Define() - Constructor for class org.anchoranalysis.bean.define.Define
 
Define() - Constructor for class org.anchoranalysis.feature.bean.list.Define
 
Define(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.Define
 
Define(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.list.Define
 
DefineAdder - Interface in org.anchoranalysis.bean.define.adder
Adds bean-definitions to a Define class
DefineAdderBean - Class in org.anchoranalysis.bean.define.adder
 
DefineAdderBean() - Constructor for class org.anchoranalysis.bean.define.adder.DefineAdderBean
 
DefineAdderUtilities - Class in org.anchoranalysis.bean.define.adder
 
DefineAdderWithPrefixBean - Class in org.anchoranalysis.bean.define.adder
Adds a prefix
DefineAdderWithPrefixBean() - Constructor for class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
 
DefinedNamed<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
 
DefinedNamed() - Constructor for class org.anchoranalysis.feature.bean.list.DefinedNamed
 
DefineFactory - Class in org.anchoranalysis.bean.define
Creates a new Define
DefineFactory() - Constructor for class org.anchoranalysis.bean.define.DefineFactory
 
DefineOutputter - Class in org.anchoranalysis.mpp.segment.bean.define
After using applying a Define on inputs, output produced entities (images, histograms, objects etc.)
DefineOutputter() - Constructor for class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
 
DefineOutputterImage - Class in org.anchoranalysis.mpp.segment.bean.define
Helper for tasks that uses a Define in association with an input to execute some tasks, and then outputs results *
DefineOutputterImage() - Constructor for class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterImage
 
DefineOutputterMPP - Class in org.anchoranalysis.mpp.segment.bean.define
 
DefineOutputterMPP() - Constructor for class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
 
DefineOutputterMPP.OperationWithInitParams<T> - Interface in org.anchoranalysis.mpp.segment.bean.define
 
DefineOutputterMPPWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define
Like a Define but outputs also MPP-related data objects and an energy-stack.
DefineOutputterMPPWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy
 
DefineOutputterMPPWithEnergy.OperationWithEnergyStack<T,​S> - Interface in org.anchoranalysis.plugin.mpp.bean.define
 
DefineOutputterWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define
 
DefineOutputterWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
 
DefineSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
 
DefineSingle() - Constructor for class org.anchoranalysis.feature.bean.list.DefineSingle
 
delegate() - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
delete(Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationDeleter
Deletes all files at this path (or any other paths derived from this one
delete(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationDeleter
 
delete(Path) - Method in class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
 
delete(BoundingBox, T) - Method in class org.anchoranalysis.spatial.rtree.RTree
 
DensityKernel - Class in org.anchoranalysis.image.voxel.kernel.density
 
DensityKernel(int, BinaryValuesByte, double) - Constructor for class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
 
deriveArray() - Method in class org.anchoranalysis.spatial.Extent
Derives an three-element array with each dimension in the extent.
deriveAssociatedFiles() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
 
deriveBoundingBox() - Method in class org.anchoranalysis.spatial.box.PointRange
 
deriveBoundingBoxNoCheck() - Method in class org.anchoranalysis.spatial.box.PointRange
Like PointRange.deriveBoundingBox() but doesn't throw an exception if no points exist.
deriveConnectedByte(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.unionfind.ConnectedComponentUnionFind
Converts binary-voxels (byte) into connected components.
deriveConnectedInt(BinaryVoxels<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.unionfind.ConnectedComponentUnionFind
Converts binary-voxels (int) into connected components.
DerivedObject - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
 
DerivedObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
 
DeriveElementsFromSequencedDirectory<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced
Derives elements of type T from a directory containing a sequence of files.
DeriveElementsFromSequencedDirectory(SequencedDirectory) - Constructor for class org.anchoranalysis.io.manifest.directory.sequenced.DeriveElementsFromSequencedDirectory
 
deriveExtent() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
 
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
 
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
 
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
 
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
 
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
 
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
 
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
 
deriveFromDelegate(FeatureInputSingleObject, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
 
deriveFromDelegate(T, U) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
 
DeriveFromPair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
Embeds each feature in a FeatureDeriveFromPair feature (first, second or merge) and prepends with a string.
DeriveFromPair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
 
deriveInputsStartBatch(ObjectCollection, EnergyStack, boolean, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
Derives a list of inputs (i.e.
deriveLabels(T, int) - Method in interface org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects.LabelsForInput
Calculates labels for a given input (and index)
deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
 
deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
 
deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.NormalizedPath
 
deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
 
deriveName(Collection<File>, String, Logger) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.patternspan.PatternSpan
 
deriveName(Collection<File>, String, Logger) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
 
deriveObject() - Method in interface org.anchoranalysis.image.core.object.seed.Seed
 
deriveObject() - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
 
deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.Mark
Create an object-mask representation of the mark (i.e.
deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
 
deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
 
deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
 
deriveObject(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
Creates an object-mask for all the voxels inside the bounding-box satisfying the predicate.
deriveObjects() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
deriveObjects(Dimensions, RegionMembershipWithFlags) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
derivePath(DerivePath, Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.PathFromGenerator
 
derivePointsLocal() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Creates a list of all ON voxels as points, using local coordinates i.e.
deriveRootedPath(Path, String, boolean, boolean) - Static method in class org.anchoranalysis.plugin.io.input.path.RootedFilePathUtilities
 
deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
 
deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
Derive scores given the value, mean and standard-deviation
deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.ZScore
 
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
 
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
 
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
 
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
 
deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
 
deriveStack(boolean) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
Derives a Stack from the display-stack that will be converted to 8-bit if necessary.
deriveStackDuplicate() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
 
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
 
deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
 
deriveSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter
Creates a new Outputter by appending a relative folder-path to the current Outputter
deriveSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing manager
deriveUnsignedBytePredicate() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes
Derives a predicate with a different interface for operating on UnsignedByteBuffer.
deriveUnsignedByteProcessor() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes
Derives a processor with a different interface for operating on UnsignedByteBuffer.
describe() - Method in class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
 
describe() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam
A string that can be displayed to the user to describe this particular SelectParam.
describe() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
 
describe() - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
 
describe() - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph
Generates a string describing the entire graph (vertices and edges)
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
 
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
 
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
 
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
 
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
 
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer
Returns a string summarizing this item
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
 
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
 
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
 
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
 
describe(boolean) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
Describes the graph in a multi-line string.
describe(String) - Method in class org.anchoranalysis.plugin.io.summarizer.FrequencyMap
 
describeAcceptedClasses() - Method in interface org.anchoranalysis.bean.initializable.property.PropertyDefiner
 
describeAcceptedClasses() - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
 
describeBean() - Method in class org.anchoranalysis.bean.AnchorBean
A (maybe longer) description identifying the bean and perhaps its key parameters.
describeBean() - Method in class org.anchoranalysis.feature.bean.Feature
 
describeBean() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
describeBean() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
 
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
 
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
 
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
 
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
 
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
describeBean() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
 
describeBean() - Method in class org.anchoranalysis.mpp.feature.mark.MarkPairCollection
 
describeBean() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
 
describeBean() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
 
describeBean() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
 
describeBean() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
 
describeChildren() - Method in class org.anchoranalysis.bean.AnchorBean
Generates a string describing the children of the current bean.
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph
Generates a string to describe a potential merge
describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
 
DescribeGraph - Class in org.anchoranalysis.plugin.image.object.merge
Logs descriptions of the graph
DescribeGraph(NeighborGraph, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.DescribeGraph
Constructor
describeLast() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
 
describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
describeMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph
 
describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
 
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
 
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
 
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
 
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
 
describeParams() - Method in class org.anchoranalysis.feature.bean.Feature
 
describeParams() - Method in class org.anchoranalysis.feature.bean.operator.Constant
 
describeParams() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
 
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
 
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
 
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
 
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
 
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
 
describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
 
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
 
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
 
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
 
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
 
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
 
describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
describeParams() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
 
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
 
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
 
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
 
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
 
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
 
describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
 
describePropertiesFriendly() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
A string that uniquely identifies all properties in the bean, but friendly to humans
describeTo(boolean) - Method in class org.anchoranalysis.core.graph.TypedEdge
Describes the edge by showing the to vertex, and optionally the payload.
description() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
A description of this directory for the manifest.
description(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
Match a file whose manifest-description has a specific function.
description(String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DirectoryMatch
 
description(String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
Match a file whose manifest-description has a specific function and type.
description(String, String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
Match a file whose manifest-description has either of two specific function and a specific type.
descriptionAndOutputName(String, String, String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
Match a file whose manifest-description has either of two specific function and a specific type and whose output-name matches a specific value.
descriptionForList(String) - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
A string description of all the items of the list concatenated together with a character in between
descriptionLong() - Method in class org.anchoranalysis.feature.bean.Feature
 
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Constant
 
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Reference
 
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Sum
 
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
 
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
 
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
 
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
 
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
 
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.NormalizedRange
 
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
 
descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
 
DescriptionMatch - Class in org.anchoranalysis.io.manifest.finder.match
 
descriptionWithCustomName() - Method in class org.anchoranalysis.feature.bean.Feature
 
DescriptiveNameContainsImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
 
DescriptiveNameContainsImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
 
DeserializationFailedException - Exception in org.anchoranalysis.core.serialize
 
DeserializationFailedException(Exception) - Constructor for exception org.anchoranalysis.core.serialize.DeserializationFailedException
 
DeserializationFailedException(String) - Constructor for exception org.anchoranalysis.core.serialize.DeserializationFailedException
 
DeserializationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.serialize.DeserializationFailedException
 
deserialize(Path) - Method in interface org.anchoranalysis.core.serialize.Deserializer
 
deserialize(Path) - Method in class org.anchoranalysis.core.serialize.KeyValueParamsDeserializer
 
deserialize(Path) - Method in class org.anchoranalysis.core.serialize.ObjectInputStreamDeserializer
 
deserialize(Path) - Method in class org.anchoranalysis.core.serialize.XStreamDeserializer
 
deserialize(Path) - Method in class org.anchoranalysis.mpp.io.marks.MarkCollectionDeserializer
 
DeserializedManifest - Class in org.anchoranalysis.plugin.io.manifest
A manifest after being deserialized from the file-system.
DeserializedManifest(File, ManifestDeserializer) - Constructor for class org.anchoranalysis.plugin.io.manifest.DeserializedManifest
 
deserializeManifest(File) - Method in interface org.anchoranalysis.io.manifest.deserializer.ManifestDeserializer
 
deserializeManifest(File) - Method in class org.anchoranalysis.io.manifest.deserializer.SimpleManifestDeserializer
 
Deserializer<T> - Interface in org.anchoranalysis.core.serialize
 
DestinationChannelForIndex - Interface in org.anchoranalysis.io.bioformats
Selects a destination-channel for the byte-copier, given an index
destinationPath(Path, Path, File, int) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
Returns the output path (destination to to be copied to) for a given single file
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
 
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
 
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.RemoveWhitespace
 
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
 
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
 
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
 
destinationPathRelative(Path, Path, File, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
 
destinationPathRelative(Path, Path, File, int) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
Calculates the relative-output path (to be appended to destDir)
destinationPathRelative(Path, Path, File, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
 
destinationPathRelative(Path, Path, File, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
 
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
 
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
Returns a list of channel-names or null if they are unavailable
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
 
determineCost() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
Merges
determineInputType(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
Finds a common input-type for two classes, throwing an exception if the two types aren't compatible.
determineInputType(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
Finds a common input-type for classes in the list, throwing an exception if any two types aren't compatible.
Develop - Class in org.anchoranalysis.plugin.mpp.experiment.bean.define
Derives various types of outputs (images, histograms etc.) from MultiInputs.
Develop() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
 
Difference - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
Difference() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Difference
 
DifferenceCalculateLevelStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.score
Similar to Difference but calculates the width as the standard-deviation of the histogram
DifferenceCalculateLevelStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
 
differenceFrom(Path, Path) - Static method in class org.anchoranalysis.core.system.path.PathDifference
Finds the difference between a path and a base
dilate(boolean, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Grow bounding-box by 1 pixel in all directions
dilate(BinaryVoxels<UnsignedByteBuffer>, boolean, int, Optional<Voxels<UnsignedByteBuffer>>, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation
 
dilate(BinaryVoxels<UnsignedByteBuffer>, int, Optional<Voxels<UnsignedByteBuffer>>, int, Optional<AcceptIterationConditon>, DilationKernelFactory) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation
Performs a morpholgical dilation operation
Dilate - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
Performs an dilation morphological operation on a binary-image
Dilate - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
Dilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
 
Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
 
DilationKernel3 - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
 
DilationKernel3(BinaryValuesByte, boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3
 
DilationKernel3ZOnly - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
 
DilationKernel3ZOnly(BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3ZOnly
 
DilationKernelFactory - Class in org.anchoranalysis.image.voxel.object.morphological
 
DilationKernelFactory(SelectDimensions, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.object.morphological.DilationKernelFactory
 
dimensionIndexFor(AxisType) - Static method in class org.anchoranalysis.spatial.axis.AxisTypeConverter
An index representing each dimension (0 for X, 1 for Y, 2 for Z)
dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStack
The image-dimensions associated with the energy-stack.
dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
 
dimensions() - Method in class org.anchoranalysis.image.core.channel.Channel
 
dimensions() - Method in class org.anchoranalysis.image.core.mask.Mask
 
dimensions() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
dimensions() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
dimensions() - Method in class org.anchoranalysis.image.core.stack.Stack
 
dimensions() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
 
dimensions() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
dimensions() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
 
dimensions() - Method in interface org.anchoranalysis.mpp.probmap.PointSampler
 
dimensions() - Method in class org.anchoranalysis.mpp.probmap.ProbMapObjects
 
dimensions() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
dimensions() - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
 
Dimensions - Class in org.anchoranalysis.image.core.dimensions
The dimensions of an image (in voxels), together with the image resolution.
Dimensions(int, int, int) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions
Construct with an explicit extent and default resolution (1.0 for each dimension)
Dimensions(Extent) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions
Construct with an explicit extent and default resolution (1.0 for each dimension)
Dimensions(Extent, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions
 
Dimensions(ReadableTuple3i) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions
Construct with an explicit extent and default resolution (1.0 for each dimension)
DimensionsChecker - Class in org.anchoranalysis.plugin.image.channel
 
DimensionsCreator - Class in org.anchoranalysis.io.bioformats
 
DimensionsCreator(IMetadata) - Constructor for class org.anchoranalysis.io.bioformats.DimensionsCreator
 
dimensionsForSeries(int) - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
 
dimensionsForSeries(int) - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
dimensionsOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
DimensionsProvider - Class in org.anchoranalysis.image.bean.provider
 
DimensionsProvider() - Constructor for class org.anchoranalysis.image.bean.provider.DimensionsProvider
 
dimensionsRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
DirectAssignMode<S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
Directly assigns a state for every optimisation step
DirectAssignMode() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
 
DirectAssignMode(ExtractScoreSize<S>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
 
DirectionVector - Class in org.anchoranalysis.image.core.orientation
 
DirectionVector() - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
 
DirectionVector(double, double, double) - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
 
DirectionVector(AxisType) - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
Creates a direction aligned to a particular axis.
DirectionVector(Tuple3d) - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
 
DirectionVectorBean - Class in org.anchoranalysis.image.bean.spatial.direction
A bean that creates a DirectionVector
DirectionVectorBean() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean
 
DirectoryDepth - Class in org.anchoranalysis.plugin.io.bean.input.files.provider
Lists all directories to a certain depth
DirectoryDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
 
DirectoryMatch - Class in org.anchoranalysis.io.manifest.finder.match
 
DirectoryStructure - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
Reuses the directories between a path and its root to form the output - and also the filename.
DirectoryStructure() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
 
DirectoryWithPrefix - Class in org.anchoranalysis.io.output.path.prefixer
 
DirectoryWithPrefix(Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
 
DirectoryWithPrefix(Path, String) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
 
dirtyInitialization() - Static method in class org.anchoranalysis.launcher.DirtyInitializer
Dirty initialisation work done that must be done every time we initialise an application that will use the Anchor platform
DirtyInitializer - Class in org.anchoranalysis.launcher
Inelegant initialisation methods that should be done in the plugins themselves, when a proper framework exists for Initialising plugins
disableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
Assigns additional outputs to disable.
DiscardOutliers - Class in org.anchoranalysis.plugin.image.bean.object.filter.dependent
Calculates features values for all objects, and discards any object less than quantile - (minRatio * stdDev)
DiscardOutliers() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
DisplayStack - Class in org.anchoranalysis.image.core.stack
Stack that contains 1 or 3 channels so that we and display it as either or RGB unsigned 8-bit image
distance(Mark, Mark) - Method in class org.anchoranalysis.mpp.bean.mark.MarkDistance
 
distance(Mark, Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceAbstractPosition
 
distance(Mark, Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceRadii
 
distance(BoundingBox, BoundingBox, boolean) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxDistance
 
distance(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d
 
distance(Point3d) - Method in class org.anchoranalysis.spatial.point.Point3d
Euclidean distance from this point to another
distance(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
distance(Point3f) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
distance(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i
 
distance(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
DistanceCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
 
DistanceCondition(Optional<UnitValueDistance>, boolean, MessageLogger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition
 
DistanceIndex - Class in org.anchoranalysis.image.core.outline.traverser.path
A distance, and the index the point came from
DistanceIndex(int, int) - Constructor for class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
 
distanceMax(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i
The maximum distance across any axis
distanceMaxToHeadTail(Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
The maximum-distance of a point to the closest contiguous-path
DistancePhysical - Class in org.anchoranalysis.image.bean.unitvalue.distance
 
DistancePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
 
distanceSquared(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d
 
distanceSquared(Point3d) - Method in class org.anchoranalysis.spatial.point.Point3d
 
distanceSquared(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
The square of the distance between two points taking account image-resolution.
distanceSquared(Point3f) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
distanceSquared(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3d
Square of Euclidean distance from this point to another
distanceSquared(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i
 
distanceSquared(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
The square of the distance between two points taking account image-resolution.
distanceSquaredTo(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
 
distanceSquaredZRelative(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
distanceSquaredZRelative(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
DistanceToContiguousPath - Class in org.anchoranalysis.image.core.outline.traverser.path
 
DistanceTransform3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
DistanceTransform3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
DistanceTransformForEachObject3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
Like DistanceTransform3D but applies the distance transform separately for each object in a collection.
DistanceTransformForEachObject3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
 
DistanceVoxels - Class in org.anchoranalysis.image.bean.unitvalue.distance
 
DistanceVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
 
DistanceVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
 
distanceZRelative(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
div(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
div(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
div(AggIDCounter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
divide(int) - Method in class org.anchoranalysis.spatial.Extent
 
Divide<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
Divide() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
 
divideBy(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
divideBy(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
divideBy(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
DivideByConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
DivideByConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
 
divideByZeroReplace(double, double, double) - Static method in class org.anchoranalysis.math.arithmetic.DoubleUtilities
Replaces a value with a constant if the divider is 0
Divider - Class in org.anchoranalysis.experiment.log
Creates a line of text that span a certain width with a repeated character, optionally containing a label.
Divider() - Constructor for class org.anchoranalysis.experiment.log.Divider
A banner using dashes.
Divider(char) - Constructor for class org.anchoranalysis.experiment.log.Divider
A banner using a particular repeated character.
DO_NOT_CHANGE_EXISTING - org.anchoranalysis.image.core.channel.convert.ConversionPolicy
 
doDuplicate(PointListBase) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
 
doesClassInheritFromAny(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.task.InputTypesExpected
Does the childclass inherit from any one of expected input-types
doesPathExist(String) - Method in class org.anchoranalysis.test.TestLoader
Does a resource exist with a particular folderPath + fileName
doesPathExist(String, String) - Method in class org.anchoranalysis.test.TestLoader
Does a resource exist with a particular folderPath + fileName
doFind(Manifest) - Method in interface org.anchoranalysis.io.manifest.finder.Finder
 
doFind(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
 
doFind(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
 
doFind(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
 
doInitFor(Object, Object, Object, Logger) - Method in interface org.anchoranalysis.bean.initializable.property.PropertyDefiner
 
doInitFor(Object, Object, Object, Logger) - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
 
doJobOnInput(InputBound<AnnotationWithStrategy<S>, AggregateSharedState>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
 
doJobOnInput(InputBound<NamedChannelsInput, SharedStateSelectedSlice>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
doJobOnInput(InputBound<NamedChannelsInput, S>) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
 
doJobOnInput(InputBound<ProvidesStackInput, GroupedSharedState<S, T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
 
doJobOnInput(InputBound<ProvidesStackInput, SharedStateFilteredImageOutput<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
 
doJobOnInput(InputBound<FileInput, CSVWriter>) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
 
doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
doJobOnInput(InputBound<MultiInput, CSVWriter>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
doJobOnInput(InputBound<MultiInput, ExperimentState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
 
doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>, SharedState<T>>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
doJobOnInput(InputBound<StackSequenceInput, SharedStateSegmentInstance<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
 
doJobOnInput(InputBound<ManifestCouplingDefinition, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
 
doJobOnInput(InputBound<FromCSVInput, FromCSVSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
 
doJobOnInput(InputBound<S, NoSharedState>) - Method in class org.anchoranalysis.experiment.bean.task.HelloWorld
 
doJobOnInput(InputBound<T, SharedStateExportFeatures<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
 
doJobOnInput(InputBound<T, Summarizer<S>>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
 
doJobOnInput(InputBound<T, S>) - Method in class org.anchoranalysis.experiment.bean.task.Task
Performs the task on a particular input.
doJobOnInput(InputBound<T, S>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
doOperation(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.mpp.feature.bean.mark.PxlListOperationFromMark
 
doSeedsIntersect() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
doSeedsIntersectWithContainingMask(ObjectMask) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
doStack(InputBound<NamedChannelsInput, NoSharedState>, NoSharedState, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
doStack(InputBound<NamedChannelsInput, NoSharedState>, OutputSequenceIndexed<Stack, String>, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
 
doStack(InputBound<NamedChannelsInput, OutputSequenceIncrementing<Stack>>, NoSharedState, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
doStack(InputBound<NamedChannelsInput, S>, U, int, int, InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
Processes one stack from a series.
dot(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
DotProductOrientationToVector - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
 
DotProductOrientationToVector() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.DotProductOrientationToVector
 
doubleFromFloat(Point2f) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
doubleFromFloat(Point3f) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
doubleFromInt(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
doubleFromInt(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
DoubleRange() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
 
DoubleUtilities - Class in org.anchoranalysis.math.arithmetic
Utilities for arithmetic operations involving type double
downcast() - Method in class org.anchoranalysis.feature.bean.Feature
Downcasts the feature
DrawLineAlongConvexHull - Class in org.anchoranalysis.plugin.imagej.bean.object.provider
Draws a lines between successive points on the convex-hull of an object.
DrawLineAlongConvexHull() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull
 
DrawObject - Class in org.anchoranalysis.overlay.bean
Draws an object-mask on a RGB-stack
DrawObject() - Constructor for class org.anchoranalysis.overlay.bean.DrawObject
 
DrawOverlay - Class in org.anchoranalysis.overlay.writer
Draws an overlay onto a RGB-stack, including precalculated overlays.
DrawOverlay() - Constructor for class org.anchoranalysis.overlay.writer.DrawOverlay
 
dropKey() - Method in exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException
Ignores the name in the exception
dropZ() - Method in class org.anchoranalysis.spatial.point.Point3d
Creates a new point with identical x and y, but with z set to 0
DualMarks - Interface in org.anchoranalysis.annotation.mark
Two mark-collections, one considered accepted and the other rejected.
DualMarksAnnotation<T> - Class in org.anchoranalysis.annotation.mark
An annotation that consists of two sets of marks, accepted and rejected.
DualMarksAnnotation() - Constructor for class org.anchoranalysis.annotation.mark.DualMarksAnnotation
 
DualStack - Class in org.anchoranalysis.mpp.segment.optimization
Stores an EnergyStack together with a background stack.
DualStack(EnergyStack) - Constructor for class org.anchoranalysis.mpp.segment.optimization.DualStack
Creates to infer a background from the energy-stack.
DualStack(EnergyStack, DisplayStack) - Constructor for class org.anchoranalysis.mpp.segment.optimization.DualStack
 
DualState<T> - Class in org.anchoranalysis.mpp.segment.optimization
Remembers the current state of type T and some best state (which was once set from the current state)
DualState() - Constructor for class org.anchoranalysis.mpp.segment.optimization.DualState
 
DualVoxelizedMarks - Class in org.anchoranalysis.plugin.mpp.segment.optimization
A transformation of one VoxelizedMarksWithEnergy into another
DualVoxelizedMarks(VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.DualVoxelizedMarks
 
DualWriterOperationRecorder - Class in org.anchoranalysis.io.manifest.operationrecorder
Allows two WriteOperationRecorder function together as if they are one
DualWriterOperationRecorder(WriteOperationRecorder, WriteOperationRecorder) - Constructor for class org.anchoranalysis.io.manifest.operationrecorder.DualWriterOperationRecorder
 
duplicate() - Method in class org.anchoranalysis.core.color.RGBColor
 
duplicate() - Method in class org.anchoranalysis.core.value.KeyValueParams
 
duplicate() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
 
duplicate() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
 
duplicate() - Method in class org.anchoranalysis.image.core.channel.Channel
 
duplicate() - Method in class org.anchoranalysis.image.core.mask.Mask
 
duplicate() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
duplicate() - Method in interface org.anchoranalysis.image.core.object.seed.Seed
 
duplicate() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
duplicate() - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
 
duplicate() - Method in class org.anchoranalysis.image.core.orientation.Orientation
 
duplicate() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
duplicate() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
duplicate() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
duplicate() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
duplicate() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
duplicate() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
 
duplicate() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
duplicate() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
duplicate() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
Immutably creates entirely new duplicated features
duplicate() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
duplicate() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
 
duplicate() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
Creates a deep copy of the current object, including deep-copying the associated buffer.
duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
Deep copy, including duplicating object-masks
duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
duplicate() - Method in class org.anchoranalysis.image.voxel.Voxels
 
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
 
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
 
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle
Deep copy the current object.
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
 
duplicate() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
 
duplicate() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
Deep-copy
duplicate() - Method in class org.anchoranalysis.math.histogram.Histogram
 
duplicate() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
 
duplicate() - Method in class org.anchoranalysis.math.moment.ImageMoments
 
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.Bound
 
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
 
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
 
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.Mark
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
duplicate() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
 
duplicate() - Method in class org.anchoranalysis.plot.AxisLimits
 
duplicate() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
Duplicate - Class in org.anchoranalysis.plugin.image.bean.channel.provider
 
Duplicate - Class in org.anchoranalysis.plugin.image.bean.mask.provider
 
Duplicate - Class in org.anchoranalysis.plugin.image.bean.object.provider
Duplicates (deep copy) an object-collection.
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
 
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
 
Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate
 
duplicateBean() - Method in class org.anchoranalysis.bean.AnchorBean
Creates a new bean that deep-copies every property value.
duplicateBean() - Method in class org.anchoranalysis.bean.define.Define
 
duplicateBean() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
duplicateBean() - Method in class org.anchoranalysis.bean.StringList
Duplicate the bean
duplicateBean() - Method in class org.anchoranalysis.bean.StringSet
Duplicate the bean
duplicateChangeExtent(Extent) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
duplicateChangeName(String) - Method in class org.anchoranalysis.feature.bean.Feature
Duplicates the feature as per AnchorBean.duplicateBean() but sets a particular custom-name
duplicateChangeResolution(Optional<Resolution>) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
duplicateChangeZ(int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
duplicateChangeZ(int) - Method in class org.anchoranalysis.spatial.Extent
 
duplicateChangeZ(int) - Method in class org.anchoranalysis.spatial.point.Point3i
 
duplicateChangeZ(int) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
 
duplicateDeep() - Method in class org.anchoranalysis.image.core.stack.Stack
Performs a deep copy of the stack, so that all channels are duplicated.
duplicateFlattenZ(int) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
duplicateForNewThread() - Method in interface org.anchoranalysis.image.feature.session.FeatureTableCalculator
Makes a copy of the feature-store for a new thread.
duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
 
duplicateFresh() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
 
duplicateHelper(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.Feature
 
duplicateHelper(KernelPosNeg<T>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
 
duplicateHelper(ConicFitterBase) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
duplicateShallow() - Method in class org.anchoranalysis.image.core.stack.Stack
Performs a shallow copy of the stack, so that all channels are reused.
duplicateShallow() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
Shallow copy of objects

E

EachObjectIndependently - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine
Simply selects features directly from the list, and objects directly from the list passed.
EachObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
 
EagerEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store
Evaluates items via their Getter as soon as they are added
EagerEvaluationStore() - Constructor for class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
 
eccentricity(double, double) - Static method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
Calculates eccentricity given two axes
EccentricityAxisAligned - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
 
EccentricityAxisAligned() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityAxisAligned
 
eccentricityForEllipsoid(double[], Orientation) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityAxisAligned
 
eccentricityForEllipsoid(double[], Orientation) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityGuessXYPlane
 
eccentricityForEllipsoid(double[], Orientation) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
Calculates eccentricity in 3D-case
EccentricityGuessXYPlane - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
 
EccentricityGuessXYPlane() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityGuessXYPlane
 
EdgeAdderParameters - Class in org.anchoranalysis.image.voxel.neighborhood
 
EdgeAdderParameters(boolean) - Constructor for class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
 
EdgeFilterIJ - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
 
EdgeFilterIJ() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ
 
edgesMaybeDuplicates() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
The edges in the graph, all of them, but with some edges possibly duplicated.
edgesUnique() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
The edges in the graph, all of them, without any duplicates.
effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
 
effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
 
effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
EigenvalueAndVector - Class in org.anchoranalysis.math.moment
An eigen-value and its corresponding eigen-vector.
EigenvalueAndVector(double, DoubleMatrix1D) - Constructor for class org.anchoranalysis.math.moment.EigenvalueAndVector
 
eigenvalueNormalizedAsAxisLength() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
A normalization of an eigen-value to represent axis-length.
eitherFunctionAndType(String, String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DescriptionMatch
 
elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
 
elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
 
elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
 
ElementSupplier<T> - Interface in org.anchoranalysis.io.output.writer
Creates or gets a element to output files together with a ElementWriter.
elementwiseOperation(ReadableTuple3i, ReadableTuple3i, IntBinaryOperator) - Static method in class org.anchoranalysis.spatial.point.Point3i
Applies an operation to each element across two points
ElementWriter<T> - Interface in org.anchoranalysis.io.output.writer
Writes an element (with or without an index) to the file system.
ElementWriterSupplier<T> - Interface in org.anchoranalysis.io.output.writer
Creates or gets a element-writer to output files.
Ellipse - Class in org.anchoranalysis.mpp.mark.conic
 
Ellipse() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse
 
Ellipse(Ellipse) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse
 
EllipseBounds - Class in org.anchoranalysis.mpp.bean.mark.bounds
 
EllipseBounds() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
 
EllipseBounds(Bound) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
 
EllipseBounds(EllipseBounds) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
 
EllipseBoundsCheck - Class in org.anchoranalysis.plugin.mpp.bean.check
 
EllipseBoundsCheck() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.EllipseBoundsCheck
 
EllipseBoundsWithoutRotation - Class in org.anchoranalysis.mpp.bean.mark.bounds
 
EllipseBoundsWithoutRotation() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
 
EllipseBoundsWithoutRotation(Bound) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
 
EllipseBoundsWithoutRotation(EllipseBoundsWithoutRotation) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
 
EllipseStandardFormConverter - Class in org.anchoranalysis.plugin.points.bean.fitter
 
EllipseStandardFormConverter(DoubleMatrix1D) - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
Ellipsoid - Class in org.anchoranalysis.mpp.mark.conic
 
Ellipsoid() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
Ellipsoid(Ellipsoid) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
EllipsoidAxisRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
 
EllipsoidAxisRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidAxisRatio
 
EllipsoidBase - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
 
EllipsoidBase() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
 
EllipsoidFactory - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
 
EllipsoidFitHelper - Class in org.anchoranalysis.plugin.points.bean.fitter
 
Ellipsoidicity - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
 
Ellipsoidicity() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipsoidicity
 
EllipsoidMaxAreaIntersectingPlane - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
 
EllipsoidMaxAreaIntersectingPlane() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidMaxAreaIntersectingPlane
 
EllipsoidOrientationRadii - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
EllipsoidOrientationRadii() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
 
EllipsoidUtilities - Class in org.anchoranalysis.mpp.mark.conic
 
Ellipticity - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
 
Ellipticity() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipticity
 
empty() - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates an empty list of features
empty() - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a newly created object-collection that is empty
Empty - Class in org.anchoranalysis.plugin.image.bean.object.provider
Creates an empty object-collection.
Empty() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Empty
 
EmptyHistogramConstant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
Specifies a constant if a histogram is empty, otherwise delegates to another {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
EmptyHistogramConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
 
enableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
Assigns additional outputs to enable.
encodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
EncodedIntBuffer - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
 
EncodedIntBuffer(UnsignedIntBuffer, WatershedEncoding) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
 
encodeDirection(int, int, int) - Method in interface org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodeDirection
 
encodeDirection(int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
EncodeDirection - Interface in org.anchoranalysis.plugin.image.segment.watershed.encoding
 
EncodedVoxels - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
 
EncodedVoxels(Voxels<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
ENCODING - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
end() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
 
end() - Method in class org.anchoranalysis.mpp.feature.bean.mark.CheckMark
end() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
 
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
 
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
 
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
 
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
 
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
 
end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
 
end() - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
 
endSeries(NoSharedState, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
endSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
 
endSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
endSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
Ends processing of a series.
ENERGY_STACK - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
 
EnergyPair - Class in org.anchoranalysis.mpp.feature.energy
 
EnergyPair(IdentifiablePair<Mark>, EnergyTotal) - Constructor for class org.anchoranalysis.mpp.feature.energy.EnergyPair
 
EnergySavedAll - Class in org.anchoranalysis.mpp.feature.energy.saved
 
EnergySavedAll() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
 
EnergySavedInd - Class in org.anchoranalysis.mpp.feature.energy.saved
 
EnergySavedInd() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
EnergySavedPairs - Class in org.anchoranalysis.mpp.feature.energy.saved
 
EnergySavedPairs(AddCriteria<EnergyPair>) - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
EnergyScheme - Class in org.anchoranalysis.mpp.feature.energy.scheme
The energy for a feature-list as factorized into different cliques.
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
 
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair, Optional<KeyValueParamsProvider>, List<NamedBean<Feature<FeatureInputStack>>>) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
 
EnergySchemeCreator - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme
 
EnergySchemeCreator() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator
 
EnergySchemeCreatorByElement - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme
 
EnergySchemeCreatorByElement() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
EnergySchemeSet - Class in org.anchoranalysis.mpp.feature.energy.scheme
A set of EnergySchemes each with a name.
EnergySchemeSet(SharedFeatureMulti) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
 
EnergySchemeWithSharedFeatures - Class in org.anchoranalysis.mpp.feature.energy.scheme
 
EnergySchemeWithSharedFeatures(EnergyScheme, SharedFeatureMulti, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
 
energyStack() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
The specified energy stack.
energyStack() - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture
 
EnergyStack - Class in org.anchoranalysis.feature.energy
An energy-stack with associated KeyValueParams.
EnergyStack(EnergyStackWithoutParams) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
 
EnergyStack(EnergyStackWithoutParams, KeyValueParams) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
 
EnergyStack(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
 
EnergyStack(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
 
EnergyStack(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
 
EnergyStack(Stack, KeyValueParams) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
 
EnergyStackWithoutParams - Class in org.anchoranalysis.feature.energy
A stack of channels used as context to calculate features (or calculating energy more broadly).
EnergyStackWithoutParams(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
Create a energy-stack comprised of a single channel
EnergyStackWithoutParams(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
Create a energy-stack with no channels - but with dimensions associated
EnergyStackWithoutParams(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
Create a energy-stack comprised of all channels from a stack
EnergyStackWriter - Class in org.anchoranalysis.mpp.io.output
Writes an energy-stack.
EnergyStackWriter(EnergyStack, Outputter) - Constructor for class org.anchoranalysis.mpp.io.output.EnergyStackWriter
 
EnergyTotal - Class in org.anchoranalysis.feature.energy
 
EnergyTotal() - Constructor for class org.anchoranalysis.feature.energy.EnergyTotal
 
EnergyTotal(double) - Constructor for class org.anchoranalysis.feature.energy.EnergyTotal
 
EnsureRegExMatch - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
Rejects files that fail to match a particular regular-expression
EnsureRegExMatch() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
 
entrySet() - Method in class org.anchoranalysis.core.identifier.name.MapCreate
 
entrySet() - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
 
equalMask(BoundingBox, int) - Method in class org.anchoranalysis.image.core.channel.Channel
 
equals(Object) - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
 
equals(Object) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
 
equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
 
equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
 
equals(Object) - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
 
equals(Object) - Method in class org.anchoranalysis.bean.shared.path.RootPath
 
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
 
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
 
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
 
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
 
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
 
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
 
equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
equals(Object) - Method in class org.anchoranalysis.core.color.RGBColor
 
equals(Object) - Method in class org.anchoranalysis.core.concurrency.WithPriority
 
equals(Object) - Method in class org.anchoranalysis.core.graph.TypedEdge
 
equals(Object) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
 
equals(Object) - Method in class org.anchoranalysis.core.index.Indexable
 
equals(Object) - Method in class org.anchoranalysis.core.log.CommonContext
 
equals(Object) - Method in class org.anchoranalysis.core.system.path.SplitPath
 
equals(Object) - Method in class org.anchoranalysis.core.value.TypedValue
 
equals(Object) - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
 
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
 
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
 
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
 
equals(Object) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
 
equals(Object) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
 
equals(Object) - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
 
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
 
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputResults
 
equals(Object) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
 
equals(Object) - Method in class org.anchoranalysis.feature.io.name.CombinedName
 
equals(Object) - Method in interface org.anchoranalysis.feature.io.name.MultiName
If another name is equal to the current name
equals(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
 
equals(Object) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
equals(Object) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
equals(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
 
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
 
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
 
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
 
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
 
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
 
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
 
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
 
equals(Object) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
equals(Object) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
equals(Object) - Method in class org.anchoranalysis.image.core.mask.Mask
 
equals(Object) - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
 
equals(Object) - Method in class org.anchoranalysis.image.core.object.MatchedObject
 
equals(Object) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation
 
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
equals(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
equals(Object) - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
 
equals(Object) - Method in class org.anchoranalysis.image.core.stack.Stack
 
equals(Object) - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
 
equals(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
 
equals(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
 
equals(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
 
equals(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
equals(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
 
equals(Object) - Method in class org.anchoranalysis.image.feature.stack.FeatureInputStack
 
equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
 
equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
 
equals(Object) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
 
equals(Object) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
 
equals(Object) - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
 
equals(Object) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
Checks if two collections are equal in a shallow way
equals(Object) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
 
equals(Object) - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
 
equals(Object) - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
 
equals(Object) - Method in class org.anchoranalysis.io.manifest.file.FileType
 
equals(Object) - Method in class org.anchoranalysis.io.manifest.ManifestDescription
 
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
 
equals(Object) - Method in class org.anchoranalysis.io.output.outputter.Outputter
 
equals(Object) - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
 
equals(Object) - Method in class org.anchoranalysis.launcher.config.HelpConfig
 
equals(Object) - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
 
equals(Object) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
 
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
 
equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
 
equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
 
equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
 
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
 
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
 
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
 
equals(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
equals(Object) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
equals(Object) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
 
equals(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
 
equals(Object) - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
 
equals(Object) - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
 
equals(Object) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
equals(Object) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
 
equals(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
 
equals(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
equals(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
 
equals(Object) - Method in class org.anchoranalysis.overlay.IndexableOverlays
 
equals(Object) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
 
equals(Object) - Method in class org.anchoranalysis.overlay.Overlay
 
equals(Object) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
 
equals(Object) - Method in class org.anchoranalysis.plot.AxisLimits
 
equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
 
equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
 
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
 
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
 
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
 
equals(Object) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
 
equals(Object) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
 
equals(Object) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
 
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
 
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
 
equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
 
equals(Object) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
equals(Object) - Method in class org.anchoranalysis.spatial.Extent
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2d
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2f
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2i
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3d
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3f
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3i
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
equals(Object) - Method in class org.anchoranalysis.spatial.point.Vector3d
 
equals(Object) - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
 
equals(Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
equals(Dimensions, boolean) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
Checks equality betwen this object and another Dimensions, maybe not comparing image-resolution.
equalsDeep(Channel, boolean) - Method in class org.anchoranalysis.image.core.channel.Channel
Are the two channels equal using a deep voxel by voxel comparison?
equalsDeep(Seed) - Method in interface org.anchoranalysis.image.core.object.seed.Seed
 
equalsDeep(Seed) - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
 
equalsDeep(Stack, boolean) - Method in class org.anchoranalysis.image.core.stack.Stack
Are the two stack equal using a deep voxel by voxel comparison of each channel?
equalsDeep(BoundedVoxels<?>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
 
equalsDeep(ObjectCollection) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
Checks if two collections are equal in a deeper way
equalsDeep(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
equalsDeep(Voxels<?>) - Method in class org.anchoranalysis.image.voxel.Voxels
Are the voxels identical to another voxels (deep equals)?
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.Mark
 
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
 
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
 
equalsDeep(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
equalsID(Object) - Method in class org.anchoranalysis.mpp.mark.Mark
 
equalsIgnoreZ(Object) - Method in class org.anchoranalysis.spatial.Extent
Checks for equality with another extent ignoring any differences in the Z dimension
equalsPrecision(double, Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
EqualTo - Class in org.anchoranalysis.math.relation
 
EqualTo() - Constructor for class org.anchoranalysis.math.relation.EqualTo
 
EqualToBean - Class in org.anchoranalysis.bean.shared.relation
 
EqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.EqualToBean
 
equalToPrimitive(Voxels<UnsignedByteBuffer>, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo
Iterates through all points with a specific voxel intensity-value, passing coordinates as primitive types.
equalToPrimitiveSlice(Voxels<UnsignedByteBuffer>, int, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo
equalToReusePoint(Voxels<UnsignedByteBuffer>, byte, Consumer<Point3i>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo
Iterates all points with a specific voxel intensity-value, reusing the Point3i in each iteration.
erode(BinaryVoxels<UnsignedByteBuffer>, boolean, int, Optional<Voxels<UnsignedByteBuffer>>, int, boolean, Optional<AcceptIterationConditon>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion
Performs a morphological erosion by dilating an inverted version of the object
Erode - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
Performs an erosion morphological operation on a binary-image
Erode - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Erode - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
 
Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
 
Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
 
Erode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
 
ErosionKernel3 - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
Erosion with a 3x3 or 3x3x3 kernel
ErosionKernel3(BinaryValuesByte, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.ErosionKernel3
 
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
 
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
 
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
 
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
 
errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
 
ErrorNode - Class in org.anchoranalysis.mpp.proposer.error
 
ErrorNode() - Constructor for class org.anchoranalysis.mpp.proposer.error.ErrorNode
 
ErrorNodeException - Exception in org.anchoranalysis.mpp.proposer.error
 
ErrorNodeException(Exception) - Constructor for exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException
 
ErrorNodeException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException
 
ErrorNodeImpl - Class in org.anchoranalysis.mpp.proposer.error
 
ErrorNodeNull - Class in org.anchoranalysis.mpp.proposer.error
Singleton that does nothing with errors
errorReporter() - Method in class org.anchoranalysis.core.log.Logger
Where errors are reported to
ErrorReporter - Interface in org.anchoranalysis.core.log.error
 
ErrorReporterForTask - Class in org.anchoranalysis.experiment.task
An error-reporter that replaces particular errors/exceptions with user-friendly messages.
ErrorReporterForTask(MessageLogger) - Constructor for class org.anchoranalysis.experiment.task.ErrorReporterForTask
 
ErrorReporterIntoLog - Class in org.anchoranalysis.core.log.error
Records errors, by writing them into a logger.
ErrorReporterIntoLog(MessageLogger) - Constructor for class org.anchoranalysis.core.log.error.ErrorReporterIntoLog
 
evalPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.Mark
 
exchange(int, EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
exchange(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
 
exchange(int, VoxelizedMarkMemo, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
exchange(EnergySavedInd, int, VoxelizedMarkMemo, EnergyStackWithoutParams, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
exchange(MemoCollection, int, VoxelizedMarkMemo, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
 
exchangeOnUpdatablePairList(ListUpdatableMarkSetCollection, Mark, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
Exclude<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
Excludes all inputs that match a regular expression
Exclude() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Exclude
 
excuteOrWait(CheckedFunction<T, S, ConcurrentModelException>) - Method in class org.anchoranalysis.core.concurrency.ConcurrentModelPool
Execute on the next available model (or wait until one becomes available)
execExperiment(String, String) - Static method in class org.anchoranalysis.test.experiment.launcher.UnitTestCompareUtilities
As we use a common format for storing our tests for the different modules.
execExperimentInTemporary(String, String, boolean, TemporaryFolder) - Static method in class org.anchoranalysis.test.experiment.launcher.UnitTestCompareUtilities
As we use a common format for storing our tests for the different modules.
execute() - Method in interface org.anchoranalysis.io.output.writer.WriterExecuteBeforeEveryOperation
Is called before every operation
execute() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
Execute the algorithm.
execute(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
 
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
 
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
 
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
 
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
 
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
 
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
 
execute(FeatureInputSingleObject, Integer) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
 
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
 
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
 
execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
 
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
 
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
The job processor is expected to remove items from the inputs-list as they are consumed so as to allow garbage-collection of these items before all jobs are processed (as the list might be quite large).
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
 
execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.SequentialProcessor
 
execute(FeatureInputAllMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
 
execute(FeatureInputAllMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
 
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
 
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
 
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
 
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
 
execute(T) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
This performs the actual calculation when needed.
execute(T) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
 
execute(T, U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
 
executeAndAssertCount(int, int, CheckedRunnable<OperationFailedException>) - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture
Executes an operation, and afterwards asserts an expected number of times certain internal methods are called on a mock-calculation.
executeEachWithMonitor(String, List<T>) - Method in class org.anchoranalysis.experiment.task.processor.MonitoredSequentialExecutor
Executes code for each element of inputs in serial, providing log-reports as to how many are finished, remain etc.
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.experiment.bean.Experiment
 
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
Executes the experiment for given arguments.
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
executeExperiment(ExperimentExecutionArguments, boolean, MessageLogger) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
Executes an experiment after finding a single experiment XML file, and reading the experiment from this file
executeExperimentWithParams(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
 
executeExperimentWithParams(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
Executes the experiment for parameters.
executeJob(ParametersUnbound<T, S>) - Method in class org.anchoranalysis.experiment.bean.task.Task
Runs the task on one particular input (a job).
executeLogStats(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
Executes the tasks, gathers statistics, and logs them
executePhase() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
Execute a single phase of the algorithm.
executingTasks() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
exists() - Method in interface org.anchoranalysis.io.manifest.finder.Finder
 
exists() - Method in class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
 
exists() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
 
exists() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
 
existsWith(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection
Does this bounding box intersect with another?
existsWithAny(List<BoundingBox>) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection
Does this bounding box intersection with any of the others in the list?
Experiment - Class in org.anchoranalysis.experiment.bean
 
Experiment() - Constructor for class org.anchoranalysis.experiment.bean.Experiment
 
ExperimentExecutionArguments - Class in org.anchoranalysis.experiment
 
ExperimentExecutionArguments() - Constructor for class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
ExperimentExecutionArguments(Path) - Constructor for class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
ExperimentExecutionException - Exception in org.anchoranalysis.experiment
An exception that occurs when an experiment is executed.
ExperimentExecutionException(String) - Constructor for exception org.anchoranalysis.experiment.ExperimentExecutionException
 
ExperimentExecutionException(String, Throwable) - Constructor for exception org.anchoranalysis.experiment.ExperimentExecutionException
A string message displayed to the user as well as a stack-trace of the cause
ExperimentExecutionException(Throwable) - Constructor for exception org.anchoranalysis.experiment.ExperimentExecutionException
 
ExperimentExecutor - Class in org.anchoranalysis.launcher.executor
Determines where the files passed the ExperimentExecutor are loaded from.
ExperimentExecutorFactory - Class in org.anchoranalysis.launcher.executor
 
ExperimentFactory - Class in org.anchoranalysis.launcher.executor.selectparam.experiment
SelectParam<Path> factory for experiments.
ExperimentIdentifier - Class in org.anchoranalysis.experiment.bean.identifier
 
ExperimentIdentifier() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifier
 
ExperimentIdentifierAuto - Class in org.anchoranalysis.experiment.bean.identifier
Automatically populates a experiment-name and version number
ExperimentIdentifierAuto() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
 
ExperimentIdentifierConstant - Class in org.anchoranalysis.experiment.bean.identifier
Defines constants for name and version of an experiment
ExperimentIdentifierConstant() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
 
ExperimentIdentifierConstant(String, String) - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
 
ExperimentLauncherFromShell - Class in org.anchoranalysis.test.experiment.launcher
Launches an experiment by calling the application 'anchor' via the shell.
ExperimentLauncherFromShell(TestLoader) - Constructor for class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
 
ExperimentResultsExperimentStructure - Class in org.anchoranalysis.plugin.quick.bean.structure
Finds some files produced in a previous experiment assuming a certain structure
ExperimentResultsExperimentStructure() - Constructor for class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
 
experimentSelectParam(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
Can point to either: a path ending in .xml, assumed to BeanXML for an experiment nothing, then default experiment is used
ExperimentState - Interface in org.anchoranalysis.mpp.segment.bean
 
ExperimentStructure - Class in org.anchoranalysis.plugin.quick.bean.structure
A file path prefixer that combines a prefix with an experimentType
ExperimentStructure() - Constructor for class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
ExportFeatureResultsAdder - Interface in org.anchoranalysis.plugin.image.task.feature
Adds results (a row in a feature-table) for export-features
ExportFeatures<T extends InputFromManager,​S,​U extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature
Calculates features and exports them as a CSV
ExportFeatures() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
 
ExportImageHistograms - Class in org.anchoranalysis.plugin.image.task.bean.grouped.histogram
Exports a histogram of voxel intensities as a CSV file for each channel of an image.
ExportImageHistograms() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
 
ExportObjectsAsCroppedImages - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
Exports a cropped image for each object-mask showing its context within an image
ExportObjectsAsCroppedImages() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
ExportObjectsBase<T extends InputFromManager,​S> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
 
ExportObjectsBase() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
 
ExportObjectsFromCSV - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
Given a CSV with a point representing an object-mask, the object-masks are extracted from a segmentation
ExportObjectsFromCSV() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
 
ExportReportFeatures - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
 
ExportReportFeatures() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
ExportReportFeaturesFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
 
ExportReportFeaturesFromManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
 
ExtendInZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
Creates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.
ExtendInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
 
ExtendInZWithinContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
Extends an object (2D/3D) as much as it can within the z-slices of a containing object
ExtendInZWithinContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
 
extendWith(int) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
Switches to extend constant-value out-of-bounds strategy
ExtensionCount - Class in org.anchoranalysis.plugin.io.bean.summarizer.path
Remembers each unique extension, and associated count
ExtensionCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
 
extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
 
extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator
Appended to the standard "serialized" extension, to form the complete extension
extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.XStreamGenerator
 
extent - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
 
extent() - Method in class org.anchoranalysis.feature.energy.EnergyStack
 
extent() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
 
extent() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
extent() - Method in class org.anchoranalysis.image.core.channel.Channel
 
extent() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
The width and height and depth of the image i.e.
extent() - Method in class org.anchoranalysis.image.core.mask.Mask
 
extent() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
extent() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
extent() - Method in class org.anchoranalysis.image.core.stack.Stack
 
extent() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
extent() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
 
extent() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
 
extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
 
extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
 
extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
 
extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
 
extent() - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
 
extent() - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
extent() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
extent() - Method in class org.anchoranalysis.image.voxel.Voxels
 
extent() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
extent() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
extent() - Method in class org.anchoranalysis.spatial.box.BoundingBox
Dimensions in pixels needed to represent the bounding box
Extent<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
Width/height/depth of energy-stack in pixels depending on axis
Extent - Class in org.anchoranalysis.spatial
Width, height etc.
Extent() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
 
Extent(int, int) - Constructor for class org.anchoranalysis.spatial.Extent
Creates with with only x and y dimensions (z dimension is assumed to be 1)
Extent(int, int, int) - Constructor for class org.anchoranalysis.spatial.Extent
Creates with x and y and z dimensions
ExtentMatchHelper - Class in org.anchoranalysis.image.voxel
 
extract() - Method in class org.anchoranalysis.image.core.channel.Channel
 
extract() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
extract() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Extracts value from voxels using global coordinates
extract() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
extract() - Method in class org.anchoranalysis.image.voxel.Voxels
Methods to read/copy/duplicate the voxel-values
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsAsFloat
 
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsAsInt
 
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsAsShort
 
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
 
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
extract(S) - Method in class org.anchoranalysis.bean.initializable.property.ExtractFromParam
 
ExtractCenterSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
Extracts the slice at the center (rounding down) of the range of z-stacks.
ExtractCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
 
extractChannel(String, boolean) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
 
extractChannel(String, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
 
extractChannel(Stack, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
 
ExtractDescriptiveName<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
 
ExtractDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveName
 
ExtractDescriptiveNameAndPath<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
 
ExtractDescriptiveNameAndPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveNameAndPath
 
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveName
 
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveNameAndPath
 
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
 
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
 
ExtractFromParam<S,​T> - Class in org.anchoranalysis.bean.initializable.property
Extracts on type of parameter from another
ExtractFromParam(Class<?>, Function<S, T>) - Constructor for class org.anchoranalysis.bean.initializable.property.ExtractFromParam
Constructor
ExtractFromParam(Class<?>, Function<S, T>, Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.ExtractFromParam
Constructor
extractFromVoxelized(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
 
extractFromVoxelized(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
 
extractFromVoxelized(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
extractKey(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
 
extractKey(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
 
extractKey(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannelsSimple
 
extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
 
extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
 
extractParamsAsDouble(KeyValueParams, String) - Static method in class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
 
ExtractPath<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
 
ExtractPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
 
extractScore(VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromVoxelizedMarksWithEnergy
 
extractScore(DualVoxelizedMarks) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromDualVoxelizedMarks
 
extractScore(ToPixelized<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.ToPixelizedExtracter
 
extractScore(T) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.ExtractScoreSize
 
ExtractScoreSize<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization
 
ExtractScoreSize() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.ExtractScoreSize
 
extractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
 
extractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
 
extractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
extractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
 
extractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
 
extractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
extractSize(VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromVoxelizedMarksWithEnergy
 
extractSize(DualVoxelizedMarks) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromDualVoxelizedMarks
 
extractSize(ToPixelized<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.ToPixelizedExtracter
 
extractSize(T) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.ExtractScoreSize
 
extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack
 
extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
 
extractSlice(int) - Method in class org.anchoranalysis.image.core.channel.Channel
Creates a new channel contain only of a particular slice (reusing the voxel buffers)
extractSlice(int) - Method in class org.anchoranalysis.image.core.mask.Mask
 
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.Stack
 
extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
extractSlice(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
extractSlice(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Extracts a particular slice.
extractSlice(int, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Extracts one particular slice as an object-mask
ExtractSlice - Class in org.anchoranalysis.plugin.image.task.bean.slice
Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice
ExtractSlice() - Constructor for class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
ExtractSliceRange - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
Extracts slices from sliceStart (inclusive) to sliceEnd (inclusive)
ExtractSliceRange() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
 
extractStack(ProvidesStackInput, StackProvider, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorRepeated
 
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
 
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
 
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
 
extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
 
extractUpToThreeChannels() - Method in class org.anchoranalysis.image.core.stack.Stack
 
extractValuesFromLeft(long) - Method in class org.anchoranalysis.math.histogram.Histogram
 
extractValuesFromRight(long) - Method in class org.anchoranalysis.math.histogram.Histogram
 
ExtractWeightFromMark - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
 
ExtractWeightFromMark() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ExtractWeightFromMark
 

F

factory() - Method in class org.anchoranalysis.image.voxel.Voxels
 
factoryParamsOnly() - Static method in class org.anchoranalysis.feature.list.NamedFeatureStoreFactory
 
FailureOnlyMessageLogger - Class in org.anchoranalysis.experiment.log
Writes text to a file, but only if FailureOnlyMessageLogger.close(boolean) is called with successful==true.
FailureOnlyMessageLogger(String, OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
 
Feature<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean
Feature that calculates a result (double) for some parameters
Feature() - Constructor for class org.anchoranalysis.feature.bean.Feature
 
Feature(PropertyInitializer<FeatureInitParams>) - Constructor for class org.anchoranalysis.feature.bean.Feature
 
FeatureAllMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
 
FeatureAllMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
 
FeatureAsIndividualProportionate - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
Calculates each feature individually, and combines them using the ratios between itemProportionate as weights
FeatureAsIndividualProportionate() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
 
FeatureCalculation<S,​T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate
Caches the result of a feature, until FeatureCalculation.invalidate() is called.
FeatureCalculation() - Constructor for class org.anchoranalysis.feature.calculate.FeatureCalculation
 
FeatureCalculationException - Exception in org.anchoranalysis.feature.calculate
 
FeatureCalculationException(String) - Constructor for exception org.anchoranalysis.feature.calculate.FeatureCalculationException
 
FeatureCalculationException(String, Throwable) - Constructor for exception org.anchoranalysis.feature.calculate.FeatureCalculationException
 
FeatureCalculationException(Throwable) - Constructor for exception org.anchoranalysis.feature.calculate.FeatureCalculationException
 
FeatureCalculationMap<S,​T extends FeatureInput,​U,​E extends Exception> - Class in org.anchoranalysis.feature.calculate
Similar to a FeatureCalculation but stores several evaluations parameterised by a key.
FeatureCalculationMap(int) - Constructor for class org.anchoranalysis.feature.calculate.FeatureCalculationMap
Creates for a particular cache-size.
FeatureCalculatorCachedMulti<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator.cached
A FeatureCalculatorMulti but calculations are cached to avoid repetition if equal FeatureInput are passed.
FeatureCalculatorCachedMulti(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
Creates a feature-calculator with a new cache
FeatureCalculatorCachedMulti(FeatureCalculatorMulti<T>, int) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
Creates a feature-calculator with a new cache
FeatureCalculatorCachedSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator.cached
A FeatureCalculatorSingle but calculations are cached to avoid repetition if equal FeatureInput are passed.
FeatureCalculatorCachedSingle(FeatureCalculatorSingle<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
Creates a feature-calculator with a new cache
FeatureCalculatorCachedSingle(FeatureCalculatorSingle<T>, int) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
Creates a feature-calculator with a new cache
FeatureCalculatorFromProvider<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
Calculates feature or feature values.
FeatureCalculatorFromProvider(ProvidesStackInput, Optional<StackProvider>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
 
FeatureCalculatorMulti<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.calculator
Calculates one or more features for given params
FeatureCalculatorMultiChangeInput<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
Likes a SequentialSession but automatically changes parameters before calculation
FeatureCalculatorMultiChangeInput(FeatureCalculatorMulti<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
Constructor
FeatureCalculatorMultiFromSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
 
FeatureCalculatorMultiFromSingle(FeatureCalculatorSingle<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
 
FeatureCalculatorMultiReuse<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
Remembers the first-calculation and always returns this value for all subsequent calculations
FeatureCalculatorMultiReuse(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
 
FeatureCalculatorRepeated - Class in org.anchoranalysis.plugin.image.task.feature.calculator
 
FeatureCalculatorSingle<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.calculator
Calculates the result of a feature for particular params
FeatureCalculatorSingleChangeInput<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
Likes a SequentialSession but automatically changes parameters before calculation
FeatureCalculatorSingleChangeInput(FeatureCalculatorSingle<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleChangeInput
 
FeatureCalculatorSingleFromMulti<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
FeatureCalculatorSingleFromMulti(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleFromMulti
 
FeatureConvertUnits<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
 
FeatureConvertUnits() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
 
FeatureConvertUnits(Feature<T>, SpatialUnits.UnitSuffix) - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
 
FeatureCostAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
 
FeatureCostAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
FeatureCSVMetadata - Class in org.anchoranalysis.feature.io.csv
What's needed to output a CSV other than the actual data items.
FeatureCSVMetadata(String, List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
 
FeatureCSVWriter - Class in org.anchoranalysis.feature.io.csv
Writes the results of feature-calculations as a CSV file.
FeatureCSVWriter(CSVWriter) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
 
FeatureDeriveFromPair - Class in org.anchoranalysis.image.feature.bean.object.pair
Base class for evaluating FeaturePairObjects in terms of another feature that operations on elements (first, second, merged etc.)
FeatureDeriveFromPair() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
FeatureDeriveFromPair(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
 
featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
 
featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
 
featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
 
featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
 
featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
 
featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromManifest
 
featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromPath
 
featureDescription(T, Logger) - Method in class org.anchoranalysis.io.output.bean.ReportFeature
 
FeatureDoubleElem<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
 
FeatureDoubleElem() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
 
FeatureEnergy<T extends FeatureInputEnergy> - Class in org.anchoranalysis.image.feature.bean
A base class for features that only require an input that extends from FeatureInputEnergy
FeatureEnergy() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureEnergy
 
FeatureEnergyChannel - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
A feature that uses a channel from the energy-stack as identified by an index
FeatureEnergyChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
 
FeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.bean.evaluator
Defines a feature and provides a means to calculate inputs for it, a session.
FeatureEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
 
FeatureHistogram - Class in org.anchoranalysis.image.feature.bean
 
FeatureHistogram() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureHistogram
 
FeatureHistogramStatistic - Class in org.anchoranalysis.image.feature.histogram
 
FeatureHistogramStatistic() - Constructor for class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
 
FeatureInitParams - Class in org.anchoranalysis.feature.calculate
Parameters used to initialize a feature before any calculations
FeatureInitParams() - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
 
FeatureInitParams(Optional<KeyValueParams>, Optional<EnergyStackWithoutParams>, Optional<SharedObjects>) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
 
FeatureInitParams(SharedObjects) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
 
FeatureInitParams(KeyValueParams) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
 
FeatureInitParams(EnergyStack) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
 
FeatureInput - Interface in org.anchoranalysis.feature.input
A single input used for feature-calculation to produce a result.
FeatureInputAllMemo - Class in org.anchoranalysis.mpp.feature.input.memo
 
FeatureInputAllMemo(MemoCollection, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
 
FeatureInputEnergy - Class in org.anchoranalysis.feature.input
 
FeatureInputEnergy() - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy
 
FeatureInputEnergy(Optional<EnergyStack>) - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy
 
FeatureInputHistogram - Class in org.anchoranalysis.image.feature.histogram
 
FeatureInputHistogram(Histogram, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.feature.histogram.FeatureInputHistogram
 
FeatureInputMark - Class in org.anchoranalysis.mpp.feature.bean.mark
 
FeatureInputMark(Mark, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
FeatureInputMark(Mark, Optional<Dimensions>, Optional<KeyValueParams>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
FeatureInputMark(Mark, Dimensions, KeyValueParams) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
FeatureInputMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection
 
FeatureInputMarkCollection(MarkCollection, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
 
FeatureInputNull - Class in org.anchoranalysis.feature.input
 
FeatureInputObjectCollection - Class in org.anchoranalysis.image.feature.object.input
 
FeatureInputObjectCollection(ObjectCollection) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
 
FeatureInputObjectCollection(ObjectCollection, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
 
FeatureInputOverlappingCircleFixture - Class in org.anchoranalysis.test.feature.plugins.objects
 
FeatureInputPairMemo - Class in org.anchoranalysis.mpp.feature.input.memo
 
FeatureInputPairMemo(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
 
FeatureInputPairObjects - Class in org.anchoranalysis.image.feature.object.input
A pair of objects (first and second) and maybe a merged version of both
FeatureInputPairObjects(FeatureInputPairObjects) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
FeatureInputPairObjects(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
FeatureInputPairObjects(ObjectMask, ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
FeatureInputParams - Interface in org.anchoranalysis.feature.input
A feature-input that is associated with particular key-value parameters
FeatureInputResults - Class in org.anchoranalysis.feature.input
 
FeatureInputResults(ResultsVectorList, FeatureNameMapToIndex) - Constructor for class org.anchoranalysis.feature.input.FeatureInputResults
 
FeatureInputSingleMemo - Class in org.anchoranalysis.mpp.feature.input.memo
 
FeatureInputSingleMemo(VoxelizedMarkMemo, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
 
FeatureInputSingleMemo(VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
 
FeatureInputSingleObject - Class in org.anchoranalysis.image.feature.object.input
An input representing a single object-mask (with maybe an energy-stack associated)
FeatureInputSingleObject(ObjectMask) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
 
FeatureInputSingleObject(ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
 
FeatureInputSingleObject(ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
 
FeatureInputStack - Class in org.anchoranalysis.image.feature.stack
 
FeatureInputStack() - Constructor for class org.anchoranalysis.image.feature.stack.FeatureInputStack
Should only be used if it's guaranteed the energy stack will be added later, as this this required.
FeatureInputStack(Optional<EnergyStackWithoutParams>) - Constructor for class org.anchoranalysis.image.feature.stack.FeatureInputStack
Params without any ImageInitParams
FeatureInputStack(EnergyStackWithoutParams) - Constructor for class org.anchoranalysis.image.feature.stack.FeatureInputStack
Params without any ImageInitParams
FeatureInputType - Class in org.anchoranalysis.feature.input
Performs checks and aggregations on feature-input types are compatible with others
FeatureInputWithResolution - Interface in org.anchoranalysis.feature.input
 
FeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
 
FeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
 
FeatureIntersectingObjectsSingleElement - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
 
FeatureIntersectingObjectsSingleElement() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
 
FeatureIntersectingObjectsThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
 
FeatureIntersectingObjectsThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold
 
FeatureList<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
A list of features with the same input-type.
FeatureList() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList
Standard Bean Constructor.
FeatureList(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList
Wraps an existing list
FeatureList(Stream<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList
Creates a list from a stream
FeatureListCSVGeneratorHorizontal - Class in org.anchoranalysis.feature.io.csv
CSV file where each feature is a column (spanning horizontally).
FeatureListCSVGeneratorHorizontal(String, FeatureNameList) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorHorizontal
Creates without setting any results (i.e.
FeatureListCSVGeneratorVertical - Class in org.anchoranalysis.feature.io.csv
CSV file where each feature is a row (spanning vertically).
FeatureListCSVGeneratorVertical(String, FeatureNameList) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorVertical
Creates without setting any results (i.e.
FeatureListElem<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
 
FeatureListElem() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureListElem
 
FeatureListElem(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureListElem
Constructor
FeatureListEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.bean.evaluator
Defines a list of features and provides a means to calculate inputs for it, a session.
FeatureListEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
 
FeatureListFactory - Class in org.anchoranalysis.feature.bean.list
Factory for creating FeatureList in different ways
FeatureListProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
 
FeatureListProvider() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureListProvider
 
FeatureListProviderAggregatePair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
Calculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.
FeatureListProviderAggregatePair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
 
FeatureListProviderLDAClassifier<T extends FeatureInput> - Class in org.anchoranalysis.plugin.ml.bean.classifier
 
FeatureListProviderLDAClassifier() - Constructor for class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
 
FeatureListProviderSVMClassifier - Class in org.anchoranalysis.plugin.ml.bean.classifier
 
FeatureListProviderSVMClassifier() - Constructor for class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
 
FeatureListStoreUtilities - Class in org.anchoranalysis.feature.list
 
FeatureMark - Class in org.anchoranalysis.mpp.feature.bean.mark
 
FeatureMark() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureMark
 
FeatureMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection
 
FeatureMarkCollection() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
 
FeatureMarkDirection - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
 
FeatureMarkDirection() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
 
FeatureMarkEccentricity - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
 
FeatureMarkEccentricity() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
 
FeatureMarkRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
 
FeatureMarkRegion() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.FeatureMarkRegion
 
FeatureNameList - Class in org.anchoranalysis.feature.name
A list of Strings representing feature names
FeatureNameList() - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
 
FeatureNameList(String) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
 
FeatureNameList(Set<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
 
FeatureNameList(Stream<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
 
FeatureNameMapToIndex - Class in org.anchoranalysis.feature.name
A map of Feature-Names (Strings) to indexes (Int)
FeatureNameMapToIndex() - Constructor for class org.anchoranalysis.feature.name.FeatureNameMapToIndex
 
featureNamesNonAggregate() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
Names of each feature in the feature columns.
FeatureObjectCollection - Class in org.anchoranalysis.image.feature.bean.object.collection
 
FeatureObjectCollection() - Constructor for class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
 
FeatureOperator<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
Base class for features that broadly accept any type of feature-input.
FeatureOperator() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureOperator
 
FeaturePairMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
 
FeaturePairMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
 
FeaturePairMemoOne - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
 
FeaturePairMemoOne() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoOne
 
FeaturePairMemoSingleRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
 
FeaturePairMemoSingleRegion() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
 
FeaturePairObjects - Class in org.anchoranalysis.image.feature.bean.object.pair
 
FeaturePairObjects() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
 
FeatureProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.provider
 
FeatureProvider() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProvider
 
FeatureProviderBean<B,​P> - Class in org.anchoranalysis.feature.bean.provider
 
FeatureProviderBean() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderBean
 
FeatureProviderDefine<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.provider
 
FeatureProviderDefine() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
 
FeatureProviderDefine(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
 
FeatureProviderReference - Class in org.anchoranalysis.feature.bean.provider
 
FeatureProviderReference() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
 
FeatureRelatedBean<T> - Class in org.anchoranalysis.feature.bean
Beans-related to features that require initialization with SharedFeaturesInitParams
FeatureRelatedBean() - Constructor for class org.anchoranalysis.feature.bean.FeatureRelatedBean
 
FeatureResults - Class in org.anchoranalysis.feature.bean.results
Features that process ResultsVectorList.
FeatureResults() - Constructor for class org.anchoranalysis.feature.bean.results.FeatureResults
 
FeatureResultSupplier - Interface in org.anchoranalysis.plugin.operator.feature.score
Supplies the result of a feature-calculation
features() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
FeatureSession - Class in org.anchoranalysis.feature.session
A single-point in the code for creating feature-sessions (a factory).
FeatureSessionCache<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
A context in which to calculate features while caching certain duplicated internal calculations among the features.
FeatureSessionCacheFactory - Interface in org.anchoranalysis.feature.session.cache
 
FeatureSessionCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
Calculates features in the context of a particular feature-session.
FeaturesFromXmlFixture - Class in org.anchoranalysis.test.feature.plugins
 
FeatureSingleMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
 
FeatureSingleMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
 
FeatureSingleMemoRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
FeatureSingleMemoRegion() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
 
FeatureSingleObject - Class in org.anchoranalysis.image.feature.bean.object.single
 
FeatureSingleObject() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
 
FeatureSingleObjectFromShared<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
Calculates as object-masks from entities in shared, using the feature-input only for a energy-stack.
FeatureSingleObjectFromShared() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
 
FeatureSource<T extends InputFromManager,​S,​U extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
Extracts features from some kind of inputs to produce one or more rows in a feature-table.
FeatureSource() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
 
FeatureStack - Class in org.anchoranalysis.image.feature.bean.stack
 
FeatureStack() - Constructor for class org.anchoranalysis.image.feature.bean.stack.FeatureStack
 
FeatureSymbolCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
Resolves and calculates a feature by a symbol (an ID/variable-name referring to another feature)
FeatureTableCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.image.feature.session
A feature-calculator with additional functions for encoding the output in in a tabular-format with column-names
FeatureTableCSVGenerator<T> - Class in org.anchoranalysis.feature.io.csv
Base class for a Generator that outputs a feature-table in CSV format.
FeatureTableCSVGenerator(String, List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureTableCSVGenerator
Creates for a particular manifest-function and headers.
FeatureTestCalculator - Class in org.anchoranalysis.test.feature.plugins
 
FeatureTestCalculatorDuo - Class in org.anchoranalysis.test.feature.plugins
Tests that consider two possibilities: positive and negative
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
 
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
 
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
 
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
 
featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
Which feature to calculate the input-value? The result is then passed to RangeCompareBase.calculateForValue(double, org.anchoranalysis.feature.calculate.cache.SessionInput<T>)
FeatureUnary<T extends FeatureInput,​S extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
A feature that contains another feature as a bean-parameter.
FeatureUnary() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
 
FeatureUnary(Feature<S>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
 
FeatureUnaryGeneric<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
A FeatureUnary that accepts any {#link FeatureInput} irrespective of type.
FeatureUnaryGeneric() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric
 
FeatureUnaryGeneric(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric
 
FeatureValueCheckMark<T extends FeatureInput> - Class in org.anchoranalysis.plugin.mpp.bean.check
 
FeatureValueCheckMark() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
FeatureValueIndividualEnergyGreaterThan - Class in org.anchoranalysis.plugin.mpp.bean.check
 
FeatureValueIndividualEnergyGreaterThan() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueIndividualEnergyGreaterThan
 
FeatureValueMarkGreaterEqualThan - Class in org.anchoranalysis.plugin.mpp.bean.check
 
FeatureValueMarkGreaterEqualThan() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueMarkGreaterEqualThan
 
FeedbackBeginParameters<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback
 
FeedbackBeginParameters() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
FeedbackEndParameters<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback
 
FeedbackEndParameters(T, MessageLogger) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
 
FeedbackReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback
 
FeedbackReceiverBean<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
 
FeedbackReceiverBean() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverBean
 
FeedbackReceiverList<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
 
FeedbackReceiverList() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
 
FeedbackReceiverRequireArguments<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
 
FeedbackReceiverRequireArguments() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
 
fetchUnmatchedWorker() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
 
fields() - Method in class org.anchoranalysis.bean.AnchorBean
A list of all bean-fields that are associated with this bean directly (fields of children are not checked).
FileDetails - Class in org.anchoranalysis.plugin.io.multifile
 
FileDetails(Path, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Constructor for class org.anchoranalysis.plugin.io.multifile.FileDetails
 
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
 
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
 
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMETiff
 
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMEXML
 
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
 
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
 
fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
 
fileInputManager() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
 
FileLabelMap<T> - Class in org.anchoranalysis.image.experiment.label
 
FileLabelMap() - Constructor for class org.anchoranalysis.image.experiment.label.FileLabelMap
 
FileMatch - Class in org.anchoranalysis.io.manifest.finder.match
 
filePath() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
FilePath - Class in org.anchoranalysis.plugin.io.bean.filepath
 
FilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.FilePath
 
FilePathAppendBase - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
 
FilePathAppendBase() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
FilePathBaseAppendToManager - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
 
FilePathBaseAppendToManager() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManager
 
FilePathBaseAppendToManagerWithFileID - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
 
FilePathBaseAppendToManagerWithFileID() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManagerWithFileID
 
FilePathCounter - Class in org.anchoranalysis.io.output.bean.path.prefixer
 
FilePathCounter() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
 
FilePathCounter(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
 
FilePathParser - Class in org.anchoranalysis.plugin.io.bean.groupfiles.parser
 
FilePathParser() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
 
FilePathPattern - Class in org.anchoranalysis.plugin.io.bean.summarizer.path
Converts a list of file-paths into a form that tries to find a pattern in the naming style using the path-pattern-finder library
FilePathPattern() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
 
FilePathPrefixerContext - Class in org.anchoranalysis.io.output.path.prefixer
 
FilePathPrefixerContext(boolean, Optional<Path>) - Constructor for class org.anchoranalysis.io.output.path.prefixer.FilePathPrefixerContext
 
FilePathResolver - Class in org.anchoranalysis.launcher
 
FilePathResolver(Class<?>) - Constructor for class org.anchoranalysis.launcher.FilePathResolver
 
FilePathToUnixStyleConverter - Class in org.anchoranalysis.core.system.path
Conversion to Unix-style separators
FileSetFromStringSet - Class in org.anchoranalysis.plugin.io.bean.provider.file
 
FileSetFromStringSet() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
 
FileSizeStatistics - Class in org.anchoranalysis.plugin.io.bean.summarizer.path
Tracks the range of file-size.
FileSizeStatistics() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
 
FileType - Class in org.anchoranalysis.io.manifest.file
 
FileType(ManifestDescription, String) - Constructor for class org.anchoranalysis.io.manifest.file.FileType
 
fill(BinaryVoxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation
 
FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider
 
FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.object.provider
Fills holes in an object.
FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
 
FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
 
filter(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Filters a ObjectCollection to include certain items based on a predicate
filter(Stream<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
Performs a Stream.filter(java.util.function.Predicate<? super T>) but accepts a predicate that can throw a checked-exception
filter(CheckedPredicate<ObjectMask, E>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Filters a ObjectCollection to include certain items based on a predicate - and optionally store rejected objects.
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.object.ObjectFilter
Filters an object-collection to remove objects according to a criteria
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
 
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
 
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
 
filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
 
Filter - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
 
Filter - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
Applies an object-filter to the results of an upstream segmentation.
Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
 
Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
 
filterAndMap(Predicate<Feature<T>>, CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
filterAndMap(Predicate<ObjectMask>, UnaryOperator<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
filterAndMapFrom(Iterable<T>, Predicate<T>, CheckedFunction<T, ObjectWithProperties, E>) - Static method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithPropertiesFactory
Creates a new collection by filtering an iterable and then mapping it to ObjectWithProperties
filterAndMapFrom(Iterable<T>, Predicate<T>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by filtering an iterable and then mapping it to ObjectMask
filterAndMapToList(List<S>, Predicate<S>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Creates a new collection by filtering a list and then mapping to a list of another type.
filterAndMapWithIndexFrom(List<T>, Predicate<T>, CheckedBiFunction<T, Integer, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by filtering a list and then mapping from it to ObjectMask.
filterAndMapWithIndexToList(List<S>, Predicate<S>, CheckedBiFunction<S, Integer, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Creates a new collection by filtering a list and then mapping (with an index) to a list of another type.
FilterByGroup - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
 
FilterByGroup() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
 
FilterCsvColumn<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter
Finds a CSV file with the names of an input as the first-column.
FilterCsvColumn() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
 
FilterDescriptiveName<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter
Filters all the input objects for only those with certain types of descriptive-names.
FilterDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
 
FilterDescriptiveNameEqualsContains - Class in org.anchoranalysis.plugin.io.input.filter
Filters a list of input-objects by the descriptive name
FilterDescriptiveNameEqualsContains(String, String) - Constructor for class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains
Constructor
filterExclude(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Filters a ObjectCollection to exclude certain items based on a predicate
FilterForExistingFiles - Class in org.anchoranalysis.plugin.io.bean.input.files.provider
 
FilterForExistingFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
 
FilterHelper - Class in org.anchoranalysis.plugin.imagej.channel.provider
 
FilterIfDebug<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter
Filters a list of inputs when in debug-mode
FilterIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
 
filterSubset(Predicate<ObjectMask>, List<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
filterToList(Collection<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Filters a collection and maps the result to a list
filterToList(Collection<T>, Predicate<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Filters a collection and maps the result to a list
finalizeBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
 
finalizeBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityByteBuffer
 
finalizeBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityShortBuffer
 
Findable<T> - Interface in org.anchoranalysis.annotation.io.image.findable
An object that can be Found or NotFound.
findArbitraryOnVoxel() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Finds any arbitrary "ON" voxel on the object.
FindChildStrategy - Interface in org.anchoranalysis.feature.session.strategy.child
 
findClosestResult(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
 
FindCommonVoxelType - Class in org.anchoranalysis.image.voxel.datatype
Finds a common voxel-data type to represent two types.
findDirectory(List<MutableDirectory>, Predicate<MutableDirectory>) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
Finder - Interface in org.anchoranalysis.io.manifest.finder
 
FinderExperimentFileDirectories - Class in org.anchoranalysis.io.manifest.finder
 
FinderExperimentFileDirectories() - Constructor for class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
 
FinderFileAsText - Class in org.anchoranalysis.io.manifest.finder
 
FinderFileAsText(String, ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderFileAsText
 
FinderKeyValueParams - Class in org.anchoranalysis.io.manifest.finder
 
FinderKeyValueParams(String, ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderKeyValueParams
 
FinderSerializedObject<T> - Class in org.anchoranalysis.io.manifest.finder
 
FinderSerializedObject(String, ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
 
FinderSingleDirectory - Class in org.anchoranalysis.io.manifest.finder
 
FinderSingleDirectory() - Constructor for class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
 
FinderSingleFile - Class in org.anchoranalysis.io.manifest.finder
 
FinderSingleFile(ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderSingleFile
 
FinderUtilities - Class in org.anchoranalysis.io.manifest.finder
 
FindFailedException - Exception in org.anchoranalysis.io.manifest.finder
 
FindFailedException(String) - Constructor for exception org.anchoranalysis.io.manifest.finder.FindFailedException
 
FindFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.manifest.finder.FindFailedException
 
findFieldsOfClass(Class<?>) - Method in class org.anchoranalysis.bean.AnchorBean
Finds all bean-fields that are instances of a certain class.
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.JobRootDirectory
 
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
 
findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.Subdirectory
 
findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderFileAsText
 
findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderKeyValueParams
 
findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
 
findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
 
findFileFromIndex(List<OutputtedFile>, String, boolean) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
findFileFromIndex(List<OutputtedFile>, String, boolean) - Method in interface org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectory
 
findIndex(String) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
findListFile(Manifest, Predicate<OutputtedFile>) - Static method in class org.anchoranalysis.io.manifest.finder.FinderUtilities
 
findListFolder(Manifest, Predicate<MutableDirectory>) - Static method in class org.anchoranalysis.io.manifest.finder.FinderUtilities
 
findMatch(ObjectCollection) - Method in class org.anchoranalysis.image.bean.object.ObjectMatcher
Finds matches for objects
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
 
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
 
findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
 
findMaxPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
 
FindMinimumDistance - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine
TODO naming is too complicated in functions with lots of min/max
findMostDeepCombinableException() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
Traverses through the nested-exceptions and finds the most deep exception that is combinable using the rules about combining and skipping outlined in the class description
findObjectsMatchingRow(ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
 
findObjectsMatchingRow(CSVRow, ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
 
findObjectsMatchingRow(CSVRow, ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
 
findObjectsMatchingRow(CSVRow, ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
 
findObjectsWithIntersectingBBox(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
findOptimum(KernelProposer<S>, ListUpdatableMarkSetCollection, FeedbackReceiver<S>, OptimizationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
 
findOptimum(KernelProposer<U>, ListUpdatableMarkSetCollection, FeedbackReceiver<S>, OptimizationContext) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.OptimizationScheme
Finds an optimal state
findOptimum(KernelProposer<U>, ListUpdatableMarkSetCollection, FeedbackReceiver<S>, OptimizationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
 
FindOutline - Class in org.anchoranalysis.image.core.outline
Finds outline voxels i.e.
FindPointOnOutline - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline
Finds a pixel on the outline of an object in a particular direction
FindPointOnOutline() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutline
 
FindPointOnOutlineWalk - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline
Walks in a particular direction until the outline is found.
FindPointOnOutlineWalk() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
 
findRoot(String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
Finds a root to match a name and debug/status
findSingleItem(Manifest, Predicate<OutputtedFile>) - Static method in class org.anchoranalysis.io.manifest.finder.FinderUtilities
 
first() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
For recording first-level outputs.
first() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
 
First - Class in org.anchoranalysis.image.feature.bean.object.pair
Evaluates the first-object in a pair only
First() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First
 
First(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First
 
FIRST - org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
 
firstConnectedTo(ContourList) - Method in class org.anchoranalysis.plugin.points.contour.ContourList
 
firstLevelContains(String) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
 
firstPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
 
firstPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName
The first part, and grouping key.
firstPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
 
firstPart() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
firstPartWithCustomMiddle(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
firstPartWithDataset() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
The first-part of the out-path string including the dataset of the current experiment as a folder
firstPartWithFilename() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
The first-part of the out-path string including the file-name of the previous experiment as a folder
FirstSecondOrderStatistic - Class in org.anchoranalysis.math.statistics
 
FirstSecondOrderStatistic() - Constructor for class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
 
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter
 
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
 
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
 
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
 
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
 
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
FitBoxToOnVoxels - Class in org.anchoranalysis.plugin.image.bean.mask.provider.resize
Fits a box around the ON pixels.
FitBoxToOnVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
 
fitMarkToPointsFromMarks(MarkCollection, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
Extract points from a marks, creates a new mark from markProvider and then fits this mark the extracted points
FitPoints - Class in org.anchoranalysis.plugin.points.bean.mark.proposer.single
 
FitPoints() - Constructor for class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
fitPointsToMark(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
FitResult - Class in org.anchoranalysis.plugin.points.bean.fitter
 
FitResult() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
flagForNoRegion() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
 
flagForRegion(int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
 
flagForRegion(int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
Combines two regions
flagForRegion(int, int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
Combines three regions
flags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
flatBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
 
flatMap(Class<? extends Exception>, CheckedFunction<ObjectMask, ObjectCollection, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Like a typical flatMap() operation but accepts a mapping function that throws a checked exception.
flatMap(Function<ObjectMask, ObjectCollection>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Creates a new ObjectCollection after mapping each item to several others.
flatMap(Optional<S>, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Like Optional.flatMap(java.util.function.Function<? super T, ? extends java.util.Optional<? extends U>>) but tolerates an exception in the mapping function, which is immediately thrown.
flatMap(Stream<S>, Class<? extends Exception>, CheckedFunction<S, Collection<? extends T>, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
Performs a Stream.flatMap(java.util.function.Function<? super T, ? extends java.util.stream.Stream<? extends R>>) but accepts a function that can throw a checked-exception
flatMapFrom(Collection<T>, Function<T, ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by flatMapping an incoming stream to ObjectCollection
flatMapFrom(Stream<T>, Class<? extends Exception>, CheckedFunction<T, ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by flatMapping an incoming stream to ObjectCollection AND rethrowing any exception during mapping
flatMapFromCollection(Stream<T>, Class<? extends Exception>, CheckedFunction<T, Collection<? extends ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new ObjectCollection by flatMapping an incoming stream to Collection<ObjectMask> AND rethrowing any exception during mapping
flatMapFromOptional(Iterable<S>, CheckedFunction<S, Optional<FeatureList<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a new feature-list by flat-mapping an iterable to an optional feature
flatMapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection
flatMapFromRange(int, int, IntFunction<ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection
flatMapToList(Collection<S>, Function<S, Stream<T>>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Flat-maps a collection to a list where in the original collection can produce many elements in the outging list.
FlattenAsChannel - Class in org.anchoranalysis.plugin.io.bean.stack.reader
Combines all series and frames returned by a reader by converting them into multiple channels in the same image
FlattenAsChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
 
flattenZ() - Method in class org.anchoranalysis.image.core.mask.Mask
 
flattenZ() - Method in interface org.anchoranalysis.image.core.object.seed.Seed
 
flattenZ() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
flattenZ() - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
 
flattenZ() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
A maximum-intensity projection (flattens in z dimension)
flattenZ() - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
flattenZ() - Method in class org.anchoranalysis.spatial.Extent
Collapses the Z dimension i.e.
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice
Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
 
FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
 
floatArray(float[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps an float-array into a voxel-buffer.
floatBuffer(FloatBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps a float buffer into a voxel-buffer.
floatFromDouble(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
floatFromInt(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
floatFromInt(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
floatFromIntDropZ(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
Creates a new Point3f with X, Y values from the Point3i but setting Z to be 0
FloatFromUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
 
FloatFromUnsignedByte() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
 
FloatFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
 
FloatFromUnsignedInt(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
 
FloatUtilities - Class in org.anchoranalysis.math.arithmetic
Utilities for arithmetic operations involving type float
FloatVoxelType - Class in org.anchoranalysis.image.voxel.datatype
 
FloodFillEachIntensityLevel - Class in org.anchoranalysis.plugin.imagej.bean.object.segment
Creates an object for each separate intensity-value (beginning at startingColor) by flood-filling.
FloodFillEachIntensityLevel() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
 
forBoxes(BoundingBox, BoundingBox) - Static method in class org.anchoranalysis.plugin.image.box.IntersectionOverUnion
Calculates the intersection-over-union score a pair of bounding-boxes.
ForceBitsPerPixel - Class in org.anchoranalysis.io.bioformats.bean.options
 
ForceBitsPerPixel() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
 
ForceChannelsPerByteArray - Class in org.anchoranalysis.io.bioformats.bean.options
 
ForceChannelsPerByteArray() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
 
ForceNumberChannels - Class in org.anchoranalysis.io.bioformats.bean.options
 
ForceNumberChannels() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
 
ForceNumberFrames - Class in org.anchoranalysis.io.bioformats.bean.options
 
ForceNumberFrames() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
 
ForceTimeSeriesToStack - Class in org.anchoranalysis.io.bioformats.bean.options
Treats a time-series as if it was a z-stack
ForceTimeSeriesToStack() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
 
forChild() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
Performs calculations not on the main cache, but on a child cache
forChild() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
 
forEach(Stream<T>, Class<? extends Exception>, CheckedConsumer<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
Performs a Stream.forEach(java.util.function.Consumer<? super T>) but accepts a consumer that can throw a checked-exception
forEach(CheckedBiConsumer<String, StoreSupplier<Stack>, E>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
Iterates over each entry in the map.
forList(List<Point3i>) - Static method in class org.anchoranalysis.image.core.points.BoundingBoxFromPoints
Create from a list of points
ForSpecificAxis<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
Dimensions-calculation for one specific axis only.
ForSpecificAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
 
forTwoPoints(Point3d, Point3d) - Static method in class org.anchoranalysis.image.core.points.BoundingBoxFromPoints
Creates a bounding-box for two unordered points.
Found<T> - Class in org.anchoranalysis.annotation.io.image.findable
A positive-result when an object is found.
Found(T) - Constructor for class org.anchoranalysis.annotation.io.image.findable.Found
 
FrequencyMap<T> - Class in org.anchoranalysis.plugin.io.summarizer
Counts the frequency of certain strings, and describes the contents in human language.
FrequencyMap() - Constructor for class org.anchoranalysis.plugin.io.summarizer.FrequencyMap
 
friendlyMessage() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
 
friendlyMessage() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
 
friendlyMessage() - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage
A friendly message to describe to the user what went wrong.
friendlyMessageHierarchy() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
 
friendlyMessageHierarchy() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
 
friendlyMessageHierarchy() - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage
A friendly message to describe to the user what went wrong, which doesn't impose a fixed-size, or showExceptionNames
friendlyMessageHierarchy(Writer, int, boolean) - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
 
friendlyMessageHierarchy(Writer, int, boolean) - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
 
friendlyMessageHierarchy(Writer, int, boolean) - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage
A friendly message to describe to the user what went wrong, including all nested exceptions that have a non-empty error message
from(Feature<T>...) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a list for one or more features
from(Channel) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus
Creates an ImagePlus from a Channel.
from(Stack, boolean) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus
Creates an ImagePlus from a Stack.
from(VoxelsWrapper) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
Converts from a VoxelsWrapper (Anchor structure) to a Img (ImgLib2 structure).
from(VoxelsWrapper) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus
Creates an ImagePlus from a VoxelsWrapper.
from(VoxelsWrapper, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
Creates a ImageProcessor by extracting a slice from a VoxelsWrapper.
FromAnnotations<T extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.file
 
FromAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
 
fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
 
fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
Creates a ImageProcessor from voxel-buffer (of type ByteBuffer) that is already a slice.
fromByte(SliceBufferIndex<UnsignedByteBuffer>, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
Creates a ImageProcessor by extracting a slice from a SliceBufferIndex of type UnsignedByteBuffer.
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
 
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg
 
FromByte - Class in org.anchoranalysis.image.voxel.factory.sliceindex
 
FromChannel - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
Creates image-dimensions by referencing them from a ChannelProvider
FromChannel - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
 
FromChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert
Creates a mask from an existing channel, reusing the channel's buffer and considering all 0 values as OFF, and 255 values as ON
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
 
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
 
FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
 
FromChannelBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider
Base-class for mask-providers that accept a channel as input
FromChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
 
FromChannelOrMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider
Creates a stack from a channel or mask (reusing the voxel buffers)
FromChannelOrMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
 
FromChannelOrMask(ChannelProvider) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
 
FromCSVInput - Class in org.anchoranalysis.plugin.mpp.experiment.objects
 
FromCSVInput(MultiInput, Path) - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
 
FromCSVInputManager - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
 
FromCSVInputManager() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
 
FromCSVSharedState - Class in org.anchoranalysis.plugin.mpp.experiment.objects
Shared-state for ExportObjectsFromCSV
FromCSVSharedState() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVSharedState
 
FromDescriptiveName - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create an output prefix
FromDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.FromDescriptiveName
 
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
 
FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider
 
FromDimensionsBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
 
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
 
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
 
FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
 
FromDualVoxelizedMarks - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
 
FromDualVoxelizedMarks() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromDualVoxelizedMarks
 
FromEntries - Class in org.anchoranalysis.plugin.io.bean.channel.map
 
FromEntries() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
 
fromFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
 
fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
 
fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg
 
FromFloat - Class in org.anchoranalysis.image.voxel.factory.sliceindex
 
FromHistogram - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
Each input-file describes a histogram that produces one row of features.
FromHistogram() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
 
FromImage - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
An image that produces one row of features.
FromImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
 
FromInput - Class in org.anchoranalysis.plugin.image.bean.channel.provider
Finds the input-stack using a conventional name of input_image - and extracts the first channel
FromInput - Class in org.anchoranalysis.plugin.image.bean.stack.provider
Finds the input-stack using a conventional name of input_image
FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
 
FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
 
FromInt - Class in org.anchoranalysis.image.voxel.factory.sliceindex
 
fromIterable(Iterable<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a list of features from an iterable
FromList - Class in org.anchoranalysis.bean.shared.color.scheme
Specifies a list of colors by a list.
FromList() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.FromList
 
FromMarkProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
 
FromMarkProposer() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
 
FromMarks - Class in org.anchoranalysis.plugin.mpp.bean.object.provider
Creates object-masks from a MarkCollection where (a particular region of) each mark creates an object.
FromMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
FromMask - Class in org.anchoranalysis.overlay.object.scaled
 
FromMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
 
FromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask
Converts a binary-mask to an object-collection (containing a single object)
FromMask() - Constructor for class org.anchoranalysis.overlay.object.scaled.FromMask
 
FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
 
FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
 
FromMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
A base class for a ChannelProvider which also uses a binary-mask, but which doesn't use any other ChannelProvider as an input.
FromMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
 
FromMetadata - Class in org.anchoranalysis.plugin.io.bean.channel.map
 
FromMetadata() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
 
fromObject(ObjectMask) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
 
FromObjects - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert
Creates a Mask from a collection of object-masks
FromObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
 
FromObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
Extracts features for each object in a collection.
FromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
 
FromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
FromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
FromOutputName - Class in org.anchoranalysis.plugin.io.bean.descriptivename
 
FromOutputName() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
 
FromParamsBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
FromParamsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
 
fromPhysicalArea(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts from physical-area to pixels.
fromPhysicalArea(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts from physical-area to pixels.
fromPhysicalDistance(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts from physical-distance to voxels.
fromPhysicalDistance(double, DirectionVector) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts from physical-distance to voxels.
fromPhysicalVolume(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts from physical-volume to voxels.
fromPhysicalVolume(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts from physical-volume to voxels.
fromProvider(Provider<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a list for a single-feature created from a provider
FromProvider - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
 
FromProvider() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
 
fromProviders(Collection<FeatureProvider<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a list of features from a collection of feature-providers
fromRepeated(int, Supplier<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by repeatedly calling a function to create a single ObjectMask
FromSerializedMarks - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
 
FromSerializedMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
 
FromSerializedObject - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
FromSerializedObject() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
 
fromSet(Set<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection from a set of ObjectMask
fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
 
fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
Creates a ImageProcessor from voxel-buffer (of type ShortBuffer) that is already a slice.
fromShort(SliceBufferIndex<UnsignedShortBuffer>, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
Creates a ImageProcessor by extracting a slice from a SliceBufferIndex of type UnsignedShortBuffer.
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
 
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg
 
FromShort - Class in org.anchoranalysis.image.voxel.factory.sliceindex
 
FromSingle - Class in org.anchoranalysis.bean.shared.color.scheme
A single color repeated to meet the size.
FromSingle() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.FromSingle
 
FromSingleMark - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
 
FromSingleMark() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
 
fromSlice(Voxels<UnsignedByteBuffer>, int, String) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus
Creates an ImagePlus from one slice of a Voxels<UnsignedByteBuffer> voxels.
fromSlice(VoxelsWrapper, int) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
 
fromStack(Stack) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
 
FromStack - Class in org.anchoranalysis.plugin.image.bean.channel.provider
Extracts a channel from a provider of a stack
FromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
 
FromStack(ProviderAsStack) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
 
FromStackChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert
 
FromStackChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
 
FromStacks - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
Selects a a subset of channels from a set of stacks
FromStacks() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks
 
fromStream(Stream<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a list of features from a stream
FromUnitValueDistance - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
 
FromUnitValueDistance() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
 
FromVoxelizedMarksWithEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
 
FromVoxelizedMarksWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromVoxelizedMarksWithEnergy
 
FromXmlList - Class in org.anchoranalysis.bean.define.adder
Adds a list of Named-Items define in a XML file in the current directory
FromXmlList() - Constructor for class org.anchoranalysis.bean.define.adder.FromXmlList
 
function(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DescriptionMatch
 
FunctionalIterate - Class in org.anchoranalysis.core.functional
Utilities for repeating operations a certain number of times.
FunctionalList - Class in org.anchoranalysis.core.functional
Utilities functions for manipulating or creating List in a functional way
FunctionalProgress - Class in org.anchoranalysis.core.functional
Utilities for updating a ProgressReporter in a functional way
functionAndType(String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DescriptionMatch
 

G

GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
 
GaussianBlur2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
 
GaussianFromParams - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
GaussianFromParams() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
 
GaussianSamplerFromParams - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
 
GaussianSamplerFromParams() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
GaussianScore<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.score
 
GaussianScore() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
 
GaussianScoreCalculator - Class in org.anchoranalysis.plugin.operator.feature.score
Calculates a Gaussian Score
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface org.anchoranalysis.mpp.feature.addcriteria.AddCriteria
 
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
 
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
 
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
 
generateIntersectingObjects(int, int, boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.IntersectingCircleObjectsFixture
Generates a number of circles that intersect and don't intersect
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
 
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.KernelIterDescriptionSerializerPeriodicReporter
 
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
 
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
 
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
 
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
 
GenerateLabelHeadersForCSV - Class in org.anchoranalysis.plugin.image.task.feature
Generates a list of header-names for columns unrelated to features (identifiers and groups)
GenerateLabelHeadersForCSV(String[], Optional<String>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.GenerateLabelHeadersForCSV
 
generateNormal(double, double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Generates a Gaussian (Normal) random variable with particular parameterization.
generateNormal(double, double) - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
 
generatePoisson(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Generates a Poisson random variable with particular parameterization.
generatePoisson(double) - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
 
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.Mark
 
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
 
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
 
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
 
generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.overlay.Overlay
 
GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider
Generates colors to match the size of an object-collection
GenerateToMatchObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
 
GenerateUniqueParameterization - Interface in org.anchoranalysis.bean
Objects that must implement well-defined equals() and hashCode() methods and also generate a name uniquely identifying the class and all parameterization
Generator<T> - Interface in org.anchoranalysis.io.generator
A class that writes a particular type of object(s) to the filesystem.
GeneratorBridge<S,​T> - Class in org.anchoranalysis.io.generator
Exposes a Generator<T> as if it was an Generator<S>.
Geometry - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
 
Geometry() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
 
Geometry(double, double) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
 
get() - Method in class org.anchoranalysis.core.cache.CachedSupplier
 
get() - Method in class org.anchoranalysis.core.concurrency.WithPriority
 
get() - Method in interface org.anchoranalysis.core.functional.checked.CheckedSupplier
Applies a supplier like with Supplier.get().
get() - Method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier
Gets the object being supplied to the store
get() - Static method in class org.anchoranalysis.core.progress.ProgressReporterNull
 
get() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
Returns the underlying feature-input (independent of the session)
get() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
 
get() - Method in interface org.anchoranalysis.feature.session.strategy.child.CacheSupplier
 
get() - Method in class org.anchoranalysis.io.manifest.finder.FinderFileAsText
 
get() - Method in class org.anchoranalysis.io.manifest.finder.FinderKeyValueParams
 
get() - Method in class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
 
get() - Method in interface org.anchoranalysis.io.manifest.finder.SerializedObjectSupplier
 
get() - Method in interface org.anchoranalysis.io.output.writer.ElementSupplier
Gets/creates the element to be written.
get() - Method in interface org.anchoranalysis.io.output.writer.ElementWriterSupplier
Gets/creates the ElementWriter to be used for an output.
get() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
 
get() - Method in class org.anchoranalysis.plugin.io.manifest.DeserializedManifest
 
get() - Method in interface org.anchoranalysis.plugin.operator.feature.score.FeatureResultSupplier
 
get(int) - Method in interface org.anchoranalysis.core.color.ColorIndex
 
get(int) - Method in class org.anchoranalysis.core.color.ColorIndexModulo
 
get(int) - Method in class org.anchoranalysis.core.color.ColorList
 
get(int) - Method in class org.anchoranalysis.core.color.SingleColor
 
get(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
 
get(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
 
get(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
 
get(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
 
get(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
 
get(int) - Method in interface org.anchoranalysis.core.index.GetterFromIndex
 
get(int) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
get(int) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
get(int) - Method in class org.anchoranalysis.feature.name.FeatureNameList
 
get(int) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
get(int) - Method in class org.anchoranalysis.feature.results.ResultsVectorList
 
get(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
get(int) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
get(int) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
get(int) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
 
get(int) - Method in class org.anchoranalysis.image.core.stack.TimeSequence
 
get(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
get(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
 
get(int) - Method in interface org.anchoranalysis.io.bioformats.DestinationChannelForIndex
 
get(int) - Method in class org.anchoranalysis.io.manifest.directory.sequenced.DeriveElementsFromSequencedDirectory
 
get(int) - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection
An individual item in the collection.
get(int) - Method in class org.anchoranalysis.math.moment.ImageMoments
 
get(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
 
get(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
get(int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
get(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
get(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
get(int) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
 
get(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
get(int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
 
get(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
get(int) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
get(int) - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
 
get(int) - Method in class org.anchoranalysis.spatial.box.BoundedList
Gets a particular element
get(int, int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
 
get(Class<? extends T>) - Method in class org.anchoranalysis.bean.BeanInstanceMap
 
get(String) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
get(String) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
 
get(String) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap
Returns null if non-existent
get(String) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
 
get(String) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
 
get(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
 
get(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.IndexedCSVRows
 
get(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.MapGroupToRow
 
get(Optional<String>) - Method in class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache
Gets (from the cache if it's already there) a context for a subdirectory of given-name
get(K) - Method in class org.anchoranalysis.core.cache.LRUCache
 
get(ProgressReporter) - Method in class org.anchoranalysis.core.progress.CachedProgressingSupplier
 
get(ProgressReporter) - Method in interface org.anchoranalysis.core.progress.CheckedProgressingSupplier
 
get(ProgressReporter) - Method in interface org.anchoranalysis.image.core.stack.NamedStacksSupplier
 
get(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer
Multiplexes one of the factories according to data-type
get(T) - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
 
get(T, int) - Method in interface org.anchoranalysis.plot.GetForSeries
 
getAboveMaxValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
Constant to return if outside the range (above the maximum allowed)
getAcceptAll() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
getAdd() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
getAddCriteria() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
getAdditionalBackgrounds() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
Additional background-stacks that are possible to use while annotating.
getAdditionalChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
Additional channels other than the main one, which are located in the main raster file
getAdditionalChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
Additional channels other than the main one, which are located in the main raster file
getAdditionalPropertyPaths() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
Additional property paths that are also changed, along with the main propertyPath *
getAddSum() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
Added to all gradients (so we can store negative gradients)
getAdjacentChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
Channels that are located in a separate raster file adjacent to the main raster file
getAfterPreoperation() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
After pre-operation but before scaling
getAggInterval() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
 
getAggIntervalLog10() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
How many iterations before printing a new report? Encoded in log10.
getAggregateReceiver() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
 
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
 
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
 
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
 
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
 
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
 
getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
 
getAggregateTriggerBank() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
getAll() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component
getAllCacheNames() - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
 
getAllKernelFactories() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
getAllowsChildren() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
getAngle() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
Angle part of axis-angle orientation (in radians)
getAngleDegrees() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
getAngleDegrees() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
 
getAngleRadians() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
getAnnealScheme() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
 
getAnnotations() - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
 
getAnnotatorStrategy() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
 
getAppendChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
Channels that are located in a separate raster file somewhere else in the project's structure
getAppendCsv() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
 
getAppendCSV() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
 
getAppendHistogram() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getAppendObjects() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
Appends object-collections to the multi-input
getAppendStack() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getArbitrary() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
getArbitraryElement() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
Gets one element of the provider (arbitrarily)
getArrange() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
 
getArrange() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
 
getAsBoolean() - Method in interface org.anchoranalysis.core.functional.checked.CheckedBooleanSupplier
Applies a supplier like with BooleanSupplier.getAsBoolean().
getAssigner() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
getAssignMode() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
 
getAssociatedElementRange() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
getAssociatedElementRange() - Method in interface org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectory
The associated element-range with ths folder.
getAssociatedMark() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
getAsSupplier(String) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
 
getAxis() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
Which axis the unit-vector will align with.
getAxis() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
Axis part of axis-angle orientation (should be normalized)
getAxis() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
 
getAxis() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
Which axis? X=0, Y=1, Z=2
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
 
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
 
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
 
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
 
getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
Which axis to read from (x,y,z)
getAxis() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
 
getAxisColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
getAxisMax() - Method in class org.anchoranalysis.plot.AxisLimits
 
getAxisMin() - Method in class org.anchoranalysis.plot.AxisLimits
 
getBackground() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
 
getBackground() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
The background
getBackground() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
The background.
getBackgroundChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
getBackgroundChannelName() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
getBackgroundChannelProvider() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
getBackgroundColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
getBackgroundID() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
getBackgroundStackMap() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
If non-null, maps underlying stack-name to a background
getBackgroundStackName() - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
 
getBeanExtension() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
getBeanExtension() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
getBeanName() - Method in class org.anchoranalysis.bean.AnchorBean
A short-name identifying a bean (by default the name of the class associated with the bean).
getBelowMinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
Constant to return if outside the range (below the minimum allowed)
getBest() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
 
getBest() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
getBestState() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getBinaryInputChannelID() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
The ID of the binary input mask that determines the region of the watershed
getBinarySgmn() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
 
getBirthRepeats() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
 
getBitsPerPixel() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
 
getBlockSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The block-size as per OpenCV implementation (identical default-size)
getBlockStride() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The block-stride as per OpenCV implementation (identical default-size)
getBlue() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
getBlue() - Method in class org.anchoranalysis.core.color.RGBColor
 
getBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
getBorderWidth() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
Adds a border around each part of the montage
getBoundCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
 
getBoundCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
getBoundRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
getBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
 
getBoundsRatio() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
getBoundType() - Method in class org.anchoranalysis.core.index.bounded.BoundChangeEvent
 
getBridgeMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
Used to match each input-object to an intermediary-object
getBundleSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
 
getBundleSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
getCache() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
 
getCache() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
 
getCache() - Method in class org.anchoranalysis.feature.session.strategy.replace.CacheAndReuseStrategy
 
getCacheNames() - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
 
getCacheSize() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
Size of feature evaluation cache for featureEvaluatorMatch
getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
 
getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
 
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
Method to calculate the level for a particular object.
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
Calculates the level for the threshold
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
 
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
 
getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
 
getCalculateLevelElse() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
 
getCalculator() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
 
getCellDefault() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
getCells() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
getCellSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The cell-size as per OpenCV implementation (identical default-size)
getCenter() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
 
getCenterPoint() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
getCenterPointX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
getCenterPointY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
getChangedMarkIDArr() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
 
getChangedMarkIDs() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getChannel() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
 
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
 
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
 
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
 
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
 
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
 
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
 
getChannel() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
A channel that is provided to the stack.
getChannel() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
 
getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack
 
getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
 
getChannel(int) - Method in class org.anchoranalysis.image.core.stack.Stack
 
getChannel(int) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
getChannel(String) - Method in class org.anchoranalysis.plugin.image.task.channel.ChannelGetterForTimepoint
 
getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
 
getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
 
getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
 
getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
 
getChannel3() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
 
getChannelAssignFrom() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
 
getChannelChecker() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState
 
getChannelConversionStyle() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
To convert as RGB or independently or in another way
getChannelConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
 
getChannelConverter() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
Optionally, how to convert from one bit-depth to another (scaling, clipping etc.)
getChannelElse() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
 
getChannelFilter() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
Optionally, includes only certain channels when converting.
getChannelFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
Index of first channel
getChannelGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
getChannelID() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
The ID of the channel that provides the input to the filter
getChannelIfVoxelZero() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
 
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
 
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
 
getChannelIndex() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
If either stackAsChannel==true or we have specified additionalChannels this indicated which channel to use from the stack
getChannelLookup() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
 
getChannelMap() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
getChannelMask() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
If defined, this is the name of channel used as a mask over the values which are fed into the histogram
getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
 
getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
By default all channels are converted into a stack.
getChannelNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
 
getChannelNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
getChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
 
getChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
 
getChannelSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
Index of second channel
getChannelsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
getChannelsPerByteArray() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
 
getChannelThreshold() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
 
getChannelType() - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
 
getChart() - Method in class org.anchoranalysis.plot.PlotInstance
 
getCheck() - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
 
getChecked() - Method in class org.anchoranalysis.io.output.outputter.Outputter
Gets the underlying delegate of Outputter that throws checked-exceptions instead of using a ErrorReporter.
getCheckMark() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
getCheckMark() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
 
getCheckMark() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
 
getCheckParsedFilePathBag() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
Imposes a condition on each parsedFilePathBag which must be-fulfilled if a file is to be included
getChildAt(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
getChildCount() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
getClassifierProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
 
getClassLoader() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
 
getClassOfTarget() - Method in class org.anchoranalysis.bean.initializable.property.ExtractFromParam
 
getCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
 
getCol() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
 
getCol(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
 
getColForListIndex(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
 
getCollection() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
 
getCollectionID() - Method in class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
 
getCollectionID() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
 
getColor() - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle
The single color to repeat.
getColor() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
An optional color associated with the label when displayed via GUI
getColor() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
 
getColor(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
getColorIDGetter() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
Gets a color ID associated with the object
getColorIndex() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
Colors for a given index
getColorList() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
getColorList() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
getColors() - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
The delegate that creates the (unshuffled) list.
getColors() - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList
The list of colors to specify
getColors() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
Colors to use for drawing objects
getColors() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
The colors in the collection.
getColorScheme() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
 
getColorsUnpaired() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
getColorUnselectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
getColumnDefinition() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
Column definition for the CSVfiles
getColumnFirstNumberPixels() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with the number of pixels for the first Object
getColumnFirstPointX() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with X coordinate of point for the first Object
getColumnFirstPointY() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with Y coordinate of point for the first Object
getColumnFirstPointZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with Z coordinate of point for the first Object
getColumnGroup() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
Name of CSV column used to group results (the same values, are outputted together)
getColumnID() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
Name of CSV column with the file identifier
getColumnNumPixels() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
Name of CSV column with the number of pixels for the first Object
getColumnPointX() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
Name of CSV column with X coordinate of point for the first Object
getColumnPointY() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
Name of CSV column with Y coordinate of point for the first Object
getColumnPointZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
Name of CSV column with Z coordinate of point for the first Object
getColumns() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
How many columns to use in the montage, or 0 to guess an approximately square output
getColumnSecondNumberPixels() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with the number of pixels for the second Object
getColumnSecondPointX() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with X coordinate of point for the first Object
getColumnSecondPointY() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with Y coordinate of point for the first Object
getColumnSecondPointZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with Z coordinate of point for the first Object
getCombine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
getCombined() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
A path that combines the directory and fileNamePrefix.
getCombined() - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
 
getCombined() - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
 
getCommand() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
One of: open, close, fill, erode, dilate, skel, outline
getCommandName() - Method in class org.anchoranalysis.launcher.config.HelpConfig
What the application command is described as in the help message e.g. anchor or anchorGUI
getComparerLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
getComparerMultiplex(boolean) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
getComparerRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
getComparers() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
getCondition() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
 
getCondition() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
 
getConfidence() - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
 
getConfidenceThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
The maximum difference in confidence for merging.
getConfigDir() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
the directory where configuration files are stored
getConnPoint() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
 
getConstant() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
 
getConstantBound() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
 
getContains() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
 
getContains() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
A descriptive-name must contain (case-sensitive) this string.
getContext() - Method in class org.anchoranalysis.core.identifier.provider.store.SharedObjects
Logger and other common configuration
getContext() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
 
getContext() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
 
getConvert() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
 
getConverters() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
getCopyFilesMethod() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
getCopyFilesNaming() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
 
getCopyFilesNaming() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
getCost() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeStrategy
 
getCost(int, int) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
Gets the cost from an element from the first-list to an element from the second-list.
getCosts() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentObjectFactory
 
getCount() - Method in class org.anchoranalysis.math.arithmetic.Counter
 
getCount() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
The running count
getCount() - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
 
getCount(int) - Method in class org.anchoranalysis.math.histogram.Histogram
 
getCountThreshold() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
getCountXY() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
The count for XY dimensions (guaranteed to always be the same
getCountZ() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
The count for Z dimension (this is identical to RunningSumPoint.getCountXY() if only 3D points have ben added)
getCreateMark() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
 
getCsvFeaturesAggregated() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
The CSV of aggregated feature-results, if enabled.
getCsvFeaturesGroup() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
The CSV individually written for each group, if enabled.
getCsvFeaturesNonAggregated() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
The CSV of non-aggregated feature-results
getCsvFilePath() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
 
getCsvFilePath() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
 
getCurrent() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
 
getCurrent() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
getCurrentTemp() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
 
getCustomName() - Method in class org.anchoranalysis.feature.bean.Feature
An optional additional name that be associated with the feature (defaults to an empty string)
getDatasetName() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
The name of the experiment including version suffix
getDatasets() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
getDatasets() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
getDatasetSpecific() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
getDatasetSpecific() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
getDatasetSuffix() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
A suffix appended to the dataset name extracted from the reg exp
getDatasetVersion() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
A version-suffix appended to the dataset name extracted from the reg exp
getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
Default values to use, if not otherwise specified
getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
 
getDefaultBeanClass() - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
Returns null as Optional is not supported by BeanFactory interface.
getDefaultColors() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
The default color-scheme used for outputs, if no other scheme is specified.
getDefaultInstances() - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
 
getDefaultInstances() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
 
getDefine() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
 
getDefine() - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
 
getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
getDefine() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Adds definitions of stacks/objects etc.
getDelaySizeAtEnd() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
getDelegate() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
 
getDelimiter() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
 
getDelta() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
getDeltat() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
getDepth() - Method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
 
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
 
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
 
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
 
getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
 
getDerivePath() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
 
getDerivePath() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
 
getDescription() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
 
getDescription() - Method in class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
 
getDescription() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
 
getDescription() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
 
getDestination() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
 
getDestination() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
 
getDestination() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.DualVoxelizedMarks
 
getDestination() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
 
getDestinationFolderPath() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
getDimensions() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
 
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
 
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
 
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
Dimensions to create new mask
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
 
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
 
getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
 
getDimensions() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
getDimensions() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
getDimensions() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
getDimensionsOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
getDimensionsRequired() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
getDimensionsSource() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
 
getDimensionsTarget() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
 
getDirection() - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
Direction of the distance being converted, defaults to a unit vector along the X-axis
getDirection() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
 
getDirectionVector() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
getDirectionVector() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
 
getDirectory() - Method in class org.anchoranalysis.core.system.path.PathDifference
The directory component of the difference, if it exists.
getDirectory() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
The directory to which the output-manager is bound to.
getDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
 
getDirectory() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
A relative-path (to the user home directory) which is used as an output directory
getDirectoryDistance() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
How many directories to recurse back from the current file to the Experiments/ directory
getDistance() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
 
getDistance() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
getDistance() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
 
getDistanceMapProvider() - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
A distance map which can also be used for making decisions on merging
getDistanceMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
 
getDistanceTransformMultiplyBy() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
Multiplies the distance transform by this factor to make it more meaningful in a short
getDistanceTransformSmoothSigmaMeters() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below
getDistanceX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
getDistanceY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
getDistanceZ() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
getDistanceZEndIfEmpty() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
getDivideByZeroValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
 
getDivisor() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
Divide by
getDivisor() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
What the identifier is divided by to find the modulo.
getDoubleOrNull(int) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
getDrawObject() - Method in class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
 
getDrawObject() - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
 
getDscr() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
 
getDscr() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
getDualStack() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
getEigenvalue() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
 
getEigenvector() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
 
getElemAllAsFeatureList() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
 
getElemAllCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
getElemByCliqueSize(int) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
 
getElement() - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
 
getElemIndAsFeatureList() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
 
getElemIndCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
getElemPairAsFeatureList() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
 
getElemPairCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
getEllipseSum(double, double, DoubleMatrix2D) - Static method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
getEllipsoidCalculator() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
getEmptyValue() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
 
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
 
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
 
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
 
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
 
getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
 
getEnd() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
An index beyond which we cannot iterate (inclusive)
getEndPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
getEnergy() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
 
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
 
getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
 
getEnergyChannelIndexCheck() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
getEnergyChannelIndexFail() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
 
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
The channel that that forms the histogram
getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
getEnergyIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
 
getEnergyIndexGradient() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
 
getEnergyIndexMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
A channel of the energyStack that is used as an additional mask using default byte values for ON and OFF
getEnergyIndexMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
Optionally, index of another channel that masks the histogram.
getEnergyIndexX() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
getEnergyIndexY() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
getEnergyIndexZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
getEnergyParamsName() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
If non-empty, A keyValueParams is treated as part of the energyStack
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
Associated Energy Scheme, which should include the EnergySavedPairs
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
 
getEnergyScheme() - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
 
getEnergyScheme() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
getEnergySchemeCreator() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
 
getEnergySchemeCreator() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Creates an energy scheme that assigns an energy score to each collection of marks.
getEnergyStack() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
 
getEnergyStack() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
getEnergyStack() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
The energy-stack
getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
 
getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
 
getEnergyStackOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
Returns the energy-stack which may or not be present
getEnergyStackRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
Returns the energy-stack or throws an exception if it's not set as it's required.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
 
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
The pre-annealed total energy
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
 
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
Pairwise energy total
getEquals() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
A descriptive-name must be exactly equal to (case-sensitive) this string.
getErrorMessage() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
getErrorNode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
getErrorReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
The associated error reporter.
getErrorReporter() - Method in class org.anchoranalysis.io.output.outputter.Outputter
 
getErrorReporter() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
 
getErrorTree() - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
 
getExactDepth() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
 
getException() - Method in exception org.anchoranalysis.core.functional.CheckedStream.ConvertedToRuntimeException
 
getException(int) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
getException(String) - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
Retrieves the item if it exists, or throws an exception if it doesn't exist.
getException(String) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
 
getException(String) - Method in class org.anchoranalysis.feature.shared.SharedFeatureSet
 
getExecutionTime() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
 
getExecutionTime() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getExperimentalManifest() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
 
getExperimentArguments() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
 
getExperimentArguments() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
 
getExperimentDescription() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
getExperimentIdentifier() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
A name for the experiment.
getExperimentIdentifier() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
 
getExperimentIdentifier() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
getExperimentManifest() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
 
getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
A folder identifying the type of experiment (where the outputs are all put in the same directory
getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
A folder identifying the type of experiment (where the outputs are all put in the same directory
getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
The value of $1 (see comment above) in naming-structure.
getExpression() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
getExtension() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
 
getExtension() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
 
getExtensionHTML() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
 
getExtensionSerialized() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
 
getExtensionText() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
 
getExtensionXML() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
 
getExtra() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
 
getExtractScoreSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
 
getExtractScoreSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
 
getExtractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
getExtractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
getExtractWeight() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
getFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
 
getFactor() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
 
getFactorHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
getFactorLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
getFactorStdDev() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
getFallback() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
getFallbackName() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
If there's no task-name, then this constant is used as a fallback name
getFeature() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
The list feature that is duplicated, and populated.
getFeature() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
 
getFeature() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
The single feature that will be calculated (possibly repeatedly) in the session
getFeature() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getFeature() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
Feature that calculates the score for an object.
getFeature() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
 
getFeature() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
 
getFeature() - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
getFeature() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
getFeatureCondition() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
 
getFeatureCondition() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
Calculates value for the condition - which is checked if it lies within a certain range
getFeatureElse() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
 
getFeatureEvaluator() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
getFeatureEvaluator() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
 
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
 
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
 
getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
 
getFeatureEvaluatorMatch() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
getFeatureEvaluatorMerge() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
 
getFeatureEvaluatorThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
Allows merge only if the feature-value satisfies a relation to this threshold
getFeatureListRef() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
 
getFeatureListSet() - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
 
getFeatureNameIndex() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
 
getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
 
getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
 
getFeatures() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
A list of providers, combined together to form a list of features, to be calculated in a session
getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
The features to be exported (after possibly some manipulation or augmentation)
getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
Features to calculate for objects in the features output.
getFeaturesAggregate() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
Features applied to each group to aggregate values (takes FeatureResultsVectorCollection)
getFeaturesImage() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Additional features that only depend on the image, so do not need to be replicated for every object.
getFeaturesPair() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Additional features that are processed on the pair of images (i.e.
getFeatureTables() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
Specifies a feature-table that can also be outputted.
getFeedbackReceiver() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
 
getFeedbackReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Processes feedback from the segmentation algorithm for outputting / debugging.
getFileExtension() - Method in class org.anchoranalysis.io.manifest.file.FileType
 
getFileFilter() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
Files to search for
getFileId() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
Unique identifier for the stack, object-mask-collection etc.
getFileId() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManagerWithFileID
Unique identifier for the stack, object-mask-collection etc.
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
 
getFileInput() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
A string indicating the input file(s)
getFilename() - Method in class org.anchoranalysis.core.system.path.PathDifference
The file-name component of the difference, if it exists.
getFileName() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
 
getFileName() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
 
getFilenamePrefix() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
 
getFilenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
 
getFilenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle
The filename to be written, including prefix, suffix, etc.
getFilenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
 
getFilenameWithoutExtension(int) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
Like IndexableOutputNameStyle.getFilenameWithoutExtension() but incorporates an integer index.
getFilenameWithoutExtension(String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
Like IndexableOutputNameStyle.getFilenameWithoutExtension() but incorporates an string index.
getFilePath() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
 
getFilePath() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
 
getFilePath() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
 
getFilePath() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
 
getFilePathParser() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
getFilePathParser() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
 
getFilePathPrefixer() - Method in class org.anchoranalysis.io.output.bean.OutputManager
Determines a prefix to use when outputting a file based upon an input-path.
getFilePathPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
 
getFilePathPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
 
getFilePathProviderSVM() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
 
getFilePrefix() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
getFiles() - Method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
 
getFilesProvider() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
getFilesProvider() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
The files to use as inputs.
getFilesProvider() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
 
getFilesProvider() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
A path to the main channel of each file
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
 
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
 
getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
 
getFilter() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
 
getFilterFilesCsv() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
If set, a CSV is read with two columns: the names of images and a
getFilterInitParams(Path) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
 
getFindOutlinePixelAngle() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
getFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
 
getFirst() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
getFirst() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
Output-names in the first-level.
getFirst() - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
First transformation from S to U
getFirst() - Method in class org.anchoranalysis.overlay.writer.PrecalculationOverlay
 
getFirst() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
 
getFirstArgument() - Method in class org.anchoranalysis.launcher.config.HelpConfig
What the application argument is described as in the help message e.g. experimentFile.xml
getFirstBinaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
getFirstBinaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
getFirstDimensions() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
getFirstExtent() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
 
getFirstPoint() - Method in class org.anchoranalysis.spatial.Contour
 
getFlatBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
 
getFloat() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
 
getFolderDataset() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
getFolderOutput() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
getFolderPath() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
 
getForAllSlices(int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
 
getForceReader() - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
If non-empty forces usage of a particular bioformats plugin
GetForSeries<T,​S> - Interface in org.anchoranalysis.plot
 
getForSlice(int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
 
getForward() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
 
getFoundDirectory() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
 
getFoundFile() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
 
getFoundOrLog(String, Logger) - Method in interface org.anchoranalysis.annotation.io.image.findable.Findable
Returns the found object (or empty() if it's not found.....
getFoundOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
 
getFoundOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
 
getFriendlyName() - Method in class org.anchoranalysis.feature.bean.Feature
 
getFriendlyName() - Method in interface org.anchoranalysis.feature.calculate.InitializableFeature
A friendly name that can be displayed to user describing the Feature.
getFrom() - Method in class org.anchoranalysis.core.graph.TypedEdge
The vertex the edge joins from.
getFuncScore() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.AccptProbCalculator
 
getFunction() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
Identifies the function the entity plays.
getGaussianSigmaMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
 
getGenerator() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
The generator to be (repeatedly) used to write elements in the sequence.
getGradient() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
getGraphColorScheme() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
getGrayscaleReconstruction() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
 
getGreen() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
getGreen() - Method in class org.anchoranalysis.core.color.RGBColor
 
getGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
getGroup() - Method in class org.anchoranalysis.feature.io.csv.RowLabels
an identifier for a higher-level group which the row belongs to (foreign key)
getGroup() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
Specifies a group for the label (similar labels that are displayed together)
getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
If non-null this file-path is used to determine the group of the file If null, no group is included.
getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
If defined, translates a file-path into a group.
getGroup() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
 
getGroup() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
 
getGroupGeneratorName() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
 
getGroupHeaders() - Method in class org.anchoranalysis.feature.io.results.LabelHeaders
Headers describing the non-feature columns outputted in the CSV related to identifying the group of a row
getGroupMap() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState
 
getGroupNum() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
 
getHeaders() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
Headers for the CSV file
getHeight() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
 
getHistogram() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
 
getHistogram() - Method in class org.anchoranalysis.image.feature.histogram.FeatureInputHistogram
 
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
An optional histogram of voxel intensity values which can be used by segment
getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
The histogram to plot.
getHistogram() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
 
getHistogram() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
getHistogramChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
 
getHistogramIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
getHistogramsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
getHistogramsOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not when outputting histograms
getHorizontalAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
 
getId() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
 
getId() - Method in class org.anchoranalysis.feature.bean.operator.Reference
 
getId() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
 
getId() - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
 
getId() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
 
getId() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
 
getId() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
 
getId() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
 
getId() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
 
getId() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
 
getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
 
getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
 
getId() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
 
getId() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
ID for the particular object-collection
getId() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
Translates an input file name to a unique ID
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
 
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
 
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
 
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
 
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
 
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
 
getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
 
getId() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
 
getId() - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
 
getIdentifier() - Method in class org.anchoranalysis.mpp.mark.Mark
 
getIdentifier() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
 
getIdentifier() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
 
getIdentifier() - Method in interface org.anchoranalysis.overlay.identifier.Identifiable
 
getIdentifier() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
 
getIdentifier(ObjectWithProperties, int) - Method in class org.anchoranalysis.image.core.object.properties.IdentifierByProperty
 
getIdentifier(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.identifier.IdentifyDelegateToOverlays
 
getIdentifier(Mark, int) - Method in class org.anchoranalysis.mpp.mark.IdentifierFromMark
 
getIdentifier(Overlay, int) - Method in class org.anchoranalysis.overlay.identifier.IdentifierFromOverlay
 
getIdentifier(T, int) - Method in interface org.anchoranalysis.core.identifier.getter.IdentifierGetter
 
getIdentifier(T, int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
 
getIdentifier(T, int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifyByIteration
 
getIdentifierSuffix() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
getIdentifierSuffix() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
getIdGenerator() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
 
getIdGetter() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
 
getIdGetter() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
Gets a unique ID associated with the object
getIfPresent(K) - Method in class org.anchoranalysis.core.cache.LRUCache
Gets an value if present, but doesn't create any new entry if it's absent.
getIgnoreContains() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
If non-empty any stackNames (after map) containing a certain string will be ignored
getImage() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
 
getImage() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getImage() - Method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
 
getImageDimensions() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
 
getImageInit() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
 
getImageLabeller() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
Maps a label to an image
getImgChannelMapCreator() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
getIncrement() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
Size of step to use when incrementing
getIncrementDegrees() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
 
getIncrementDegrees() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
getIndex() - Method in class org.anchoranalysis.core.index.Indexable
 
getIndex() - Method in interface org.anchoranalysis.core.index.IndexGetter
 
getIndex() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
 
getIndex() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
 
getIndex() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
 
getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
 
getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
Index in z-dimension of slice to extract
getIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
getIndex() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
getIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
 
getIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
 
getIndex() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
Which index to return from the HOG descriptor
getIndex(String) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
getIndex(TreeNode) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
getIndexedRowsOrCreate(Path, ColumnDefinition) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVSharedState
 
getIndexForMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
getIndexNonZero() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
getIndividual() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
getInitContext() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
getInitializationParameters() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
 
getInitialKernel() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
getInitialPoint() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
 
getInitParams() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
 
getInitParamType() - Method in class org.anchoranalysis.bean.initializable.property.PropertyInitializer
 
getInnerCoreDistance() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
getInPathPrefix() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
 
getInput() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
 
getInput() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
The input-manager to specify where/which/how necessary inputs for the experiment occur.
getInput() - Method in class org.anchoranalysis.experiment.task.InputBound
 
getInput() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
 
getInput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
 
getInput() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getInput() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
getInput() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
 
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
 
getInput() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
 
getInputDebug() - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
 
getInputDirectory() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
A directory indicating where inputs can be located
getInputFilterExtensions() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
If defined, a set of extension filters that can be applied on inputDirectory
getInputIfPresent(T) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
 
getInputName() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getInputName() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
getInputName() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
 
getInputOutputContext() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
getInputPaths() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
getInputPointShift() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
getInstance() - Static method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
 
getInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
Gets an element from the buffer at a particular position, converting, if necessary, to an int.
getInt(int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
getInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
getIntensity() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
getIntensityHistogram() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
 
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
 
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
Interpolator used when scaling the background
getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
 
getItem() - Method in class org.anchoranalysis.bean.NamedBean
The item that is to be named (i.e.
getItem() - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
 
getItem() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
 
getItem() - Method in class org.anchoranalysis.feature.bean.list.PrependName
 
getItem() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
 
getItem() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
getItem() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
 
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
 
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
 
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
For each feature in the list, a corresponding "aggregate" feature is created in the output list
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
Feature to apply to the histogram
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
 
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
 
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
 
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
 
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
 
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
Feature to apply to the histogram
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
 
getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
 
getItem() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
 
getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
 
getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
 
getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
Feature to apply to the histogram
getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoOne
 
getItem1() - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
 
getItem2() - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
 
getItemMean() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
 
getItemProportionate() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
 
getItemStdDev() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
 
getIteration() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getIterations() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
 
getIterations() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
The maximum number of iterations.
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
The number of dilations and erosions to apply to determine if two objects intersect
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
The number of dilations and erosions to apply and whether to do in the Z dimension
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
 
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
 
getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
The number of dilations and erosions to apply and whether to do in the Z dimension
getIterations() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
iterations for erode, dilate, open, close
getIterations() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
 
getIterationsDilation() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
Number of times to perform morphological dilation
getIterationsErosion() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
Number of times to perform morphological erosion
getJobDescription() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob
 
getJobManifest() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
 
getJobNumber() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
 
getJobShortName() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
 
getJobState() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob
 
getKappa() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
getKeep() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
 
getKeepProcessorsFree() - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
How many processors to avoid using for the tasks.
getKeepProcessorsFree() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
How many processors to avoid using for the tasks.
getKernel() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
 
getKernel() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
 
getKernel() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
getKernel() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
 
getKernelAccepted() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
getKernelCalcContext() - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
 
getKernelFactoryList() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
getKernelHalfWidth() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
getKernelNegative() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
getKernelNoProposalDescription() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getKernelPositive() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
getKernelProposed() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
getKernelProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Proposes kernel-changes during iterations of hte marked-point-processes.
getKernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
getKey() - Method in exception org.anchoranalysis.core.index.GetOperationFailedException
 
getKey() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
 
getKey() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
getKey() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
 
getKey() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
 
getKey() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
 
getKey() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
getKey() - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
 
getKeyGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
getKeyLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
getKeyMean() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
 
getKeyPrefix() - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
Prefix prepended to key
getKeyStdDev() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
 
getKeySuffix() - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
 
getKeyUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
getKeyValueParams() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
 
getKeyValueParamsID() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
 
getKeyValueParamsID() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
If non-empty, the identifier of a key-value-params collection that is passed to the segmentation procedure.
getLabel() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
The label that applies to the image
getLabelMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
 
getLabels() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
getLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
 
getLast() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
 
getLastDivider() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
getLastPoint() - Method in class org.anchoranalysis.spatial.Contour
 
getLastPoints1() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
 
getLastPoints2() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
 
getLeafDirectories() - Method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
 
getLeft() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
Objects on left-side of the comparison
getLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
 
getLevel() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
 
getLine() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
 
getList() - Method in class org.anchoranalysis.bean.define.adder.Concatenate
 
getList() - Method in class org.anchoranalysis.bean.shared.regex.RegExList
 
getList() - Method in class org.anchoranalysis.bean.shared.StringMap
 
getList() - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple
The list of loggers to log to
getList() - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
 
getList() - Method in class org.anchoranalysis.feature.bean.list.Define
 
getList() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
 
getList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
getList() - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
 
getList() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
 
getList() - Method in class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
 
getList() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
getList() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
 
getList() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
 
getList() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
 
getList() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
 
getList() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
 
getList() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine
A list of other filters from which the sub-classes implement filtering behaviour.
getList() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
 
getList() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
getList() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
 
getList() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
 
getList() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
 
getList() - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
 
getList() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Combine
 
getList() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
 
getList() - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
 
getList() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
 
getList() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
 
getList() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
 
getList(Class<?>) - Method in class org.anchoranalysis.bean.define.Define
 
getListAdditionalChannelProviders() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
 
getListAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
getListAppend() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
Additional entities that are appended to the multi-input
getListAppendFilePath() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getListAppendKeyValueParams() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getListAppendMarks() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getListAppendMarksFromAnnotation() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getListAppendMarksFromAnnotationAcceptedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getListAppendMarksFromAnnotationRejectedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getListComparers() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
getListFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
 
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendFilePath
 
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
 
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
 
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendMarks
 
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendObjects
 
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
 
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
 
getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManager
 
getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
 
getListPaired(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
 
getListPaired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
 
getListPaired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
getListReportFeatures() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
getListReportFeatures() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
 
getListStackProvider() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
The channels we extract the object-masks from - all assumed to be of same dimension
getListStackProviderMIP() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
The channels we extract the object-masks from - all assumed to be of same dimension
getListUnassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
 
getListUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
 
getListUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
getListUnassignedLeft() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
getListUnassignedRight() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
getLocal(int) - Method in class org.anchoranalysis.image.voxel.kernel.LocalSlices
 
getLocalPath() - Method in class org.anchoranalysis.bean.AnchorBean
A local path on the filesystem associated with this bean (from serialization) if defined.
getLog() - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
The logger to use if conditions are fulfilled
getLog() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
getLogExperiment() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
Where log messages that do not pertain to a specific job (input) appear.
getLogExperimentPath() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
Relative path to a logger for the experiment in gneeral
getLogger() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
The logger
getLogger() - Method in class org.anchoranalysis.core.log.CommonContext
The logger
getLogger() - Method in class org.anchoranalysis.experiment.task.InputBound
 
getLogger() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
 
getLogger() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
The associated logger.
getLogger() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
 
getLogger() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
 
getLogger() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
getLogger() - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
 
getLogger() - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
 
getLogger() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
 
getLoggerExperiment() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
 
getLoggerTaskCreator() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
 
getLogReporterJob() - Method in class org.anchoranalysis.experiment.task.InputBound
 
getLogTask() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
Where log messages that do pertain to a specific job (input) appear.
getLogTaskPath() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
Relative path to a logger for a specific task
getLookup() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
 
getMainChannelIndex() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
Index of the mainChannel
getMainChannelName() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
The name of the channel provided by the rasters in file Provider
getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
 
getMajorAxisAngle() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
getMajorAxisSlope() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
getManifest() - Method in class org.anchoranalysis.experiment.task.InputBound
 
getManifestDescription() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
A manifest-description for the directory, if defined.
getManifestDescription() - Method in class org.anchoranalysis.io.manifest.file.FileType
 
getManifestDescriptionFunction() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
 
getManifestDeserializer() - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
getManifestExperimentInputFileSet() - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
getManifestFunction() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
 
getManifestFunction() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
getManifestInputFileSet() - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
getMap() - Method in class org.anchoranalysis.mpp.io.input.OperationMap
 
getMap() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
 
getMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
 
getMark() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
getMark() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
The associated mark
getMark() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
 
getMark() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
 
getMark() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
 
getMarkBounds() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
Backwards compatible for when we only had a single bounds
getMarkBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
 
getMarkBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
 
getMarkBoundsSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getMarkEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
A mark-evaluator that is added to the GUI to support this annotation
getMarkFactory() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
 
getMarkFactory() - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
 
getMarkFactory() - Method in class org.anchoranalysis.mpp.segment.kernel.MarkFactoryContext
 
getMarkFactory() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
getMarkFactory() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Creates a new mark, before perhaps further manipulations by a kernel.
getMarkFactory() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
 
getMarkFromMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
getMarkMergeProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getMarkProposer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
Name of the MarkProposer to use.
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
 
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
 
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
 
getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
 
getMarkProposerAdditionalBirth() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
getMarkProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getMarkProvider() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
 
getMarkProvider() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
 
getMarkProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
 
getMarkProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
getMarkProvider() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
getMarkRmv() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
 
getMarks() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
getMarks() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
 
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
 
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
The marks
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
getMarks() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
 
getMarks() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
 
getMarks() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
getMarks() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
 
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
 
getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
 
getMarks() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
 
getMarksAfter() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getMarksAfterOptional() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getMarksCollection() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getMarksColored() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
getMarksOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not when outputting configurations
getMarkSplitProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
getMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
 
getMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
getMarksProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getMarksReject() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
Marks covering area that should be rejected, can be null
getMarksWithTotalEnergy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
getMask() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
An optional mask which restricts the algorithm to only parts of the channel where the mask has an ON voxel
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
 
getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
A mask that is provided to the stack.
getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
 
getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
 
getMask() - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
 
getMask() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
 
getMask() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
 
getMask() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
getMaskElse() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
Returned instead of mask if the predicate is not satisfied
getMaskFilled() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
getMaskFilled() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
getMaskIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
 
getMaskOutline() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
getMaskValue() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
What voxel value to read as "On" in the mask above.
getMaskValue() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
 
getMatch() - Method in class org.anchoranalysis.feature.bean.list.SelectFromShared
 
getMatch() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
 
getMatch() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
 
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
 
getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
 
getMatches() - Method in class org.anchoranalysis.image.core.object.MatchedObject
The matches associated with the source-object
getMatchString() - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
 
getMatrix() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
A two-dimensional array mapping the costs from first to second
getMatrix() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
getMavenProperties() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
 
getMax() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
 
getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
 
getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
 
getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
 
getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
 
getMax() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
getMax() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
getMax() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
 
getMax() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
 
getMax() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
 
getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
Maximum-boundary for acceptable range
getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
 
getMax() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
 
getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
Calculates maximally-allowed range boundary
getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
Boundary value indicating maximally-allowed range value
getMaxBin() - Method in class org.anchoranalysis.math.histogram.Histogram
Maximum bin-value inclusive
getMaxCost() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
getMaxCost() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
getMaxDirectoryDepth() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
 
getMaxDistance() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
An optional maximum distance
getMaxDistance() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
 
getMaxDistance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
 
getMaxDistanceBetweenMinima() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
 
getMaxDistanceCOG() - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
The maximum distance allowed between center-of-gravities of objects
getMaxDistanceDeltaContour() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
The maximum distance allowed between two seeds in terms of their values in the distance map
getMaxDistanceDeltaContour() - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
The maximum distance allowed between the 'distance from contour' values provided from the distanceMap for each point.
getMaxDistanceProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
 
getMaxDistanceZ() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
 
getMaximumIndex() - Method in interface org.anchoranalysis.core.index.bounded.BoundedRange
 
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
 
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
 
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
 
getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
 
getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
 
getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
 
getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
 
getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
 
getMaxNumber() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
 
getMaxNumberItems() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Limit
 
getMaxNumberProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
getMaxNumberProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
Theoretical maximum number of (CPU) processors to use in parallel.
getMaxNumberProcessors() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
getMaxNumberProcessors() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
getMaxNumItems() - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
 
getMaxNumItems() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
 
getMaxOfMax() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
 
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
 
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
 
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
 
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds
 
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
 
getMaxSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
getMaxSplitGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
getMaxValue() - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
 
getMaxVar() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
getMaxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
 
getMaxX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Maximum X coordinate inclusive
getMaxY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Maximum Y coordinate inclusive
getMaxZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Maximum Z coordinate inclusive
getMean() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
Mean
getMean(int) - Method in class org.anchoranalysis.math.moment.ImageMoments
Index is the axis (0 for X, 1 for Y, 2 for Z)
getMedianRadiusMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
 
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
getMemoForIndex(int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex
 
getMemoForMark(Mark) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
getMemoForMark(MarkCollection, Mark) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
getMemoized() - Method in class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
Provides a memoized (cached) means of access the results of the finder
getMerge() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
 
getMerged() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
Returns a merged version of the two-objects available (or null if not available)
getMergedOptional() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
getMergedPosTolerance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
 
getMergeMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
getMessage() - Method in exception org.anchoranalysis.core.index.GetOperationFailedException
 
getMessage() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
 
getMessageLogger() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
Exposed as StatefulMessageLogger rather than as MessageLogger that is found in Logger
getMessageReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
The associated message reporter.
getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
 
getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string for the default).
getMiddlePoint() - Method in class org.anchoranalysis.spatial.Contour
 
getMin() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
 
getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
 
getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
 
getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
 
getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
 
getMin() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
getMin() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
getMin() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
 
getMin() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
 
getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
Minimum-boundary for acceptable range
getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
 
getMin() - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
 
getMin() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
Calculates minimally-allowed range boundary
getMin() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
Boundary value indicating minimally-allowed range value
getMin(Function<FileDetails, Optional<Integer>>) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
 
getMinConfidence() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
The minimum confidence of an element for its object-mask to be included.
getMinConfidence() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
Proposed bounding boxes below this confidence interval are removed
getMinDiff() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
 
getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
A minimum difference, below which 0.0 is returned
getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
 
getMinDiversity() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
getMinimaImposition() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
 
getMinimumBoundingBoxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
Only objects whose bounding-box volume is greater or equal to this threshold are included.
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
 
getMinimumIndex() - Method in interface org.anchoranalysis.core.index.bounded.BoundedRange
 
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
 
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
 
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
 
getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
 
getMinIntensity() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
 
getMinIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
Intensity for thresholding
getMinIntensityValue() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
getMinMaxIgnoreBeforeIndex() - Method in class org.anchoranalysis.plot.index.LinePlot
 
getMinNumberObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
getMinNumberPoints() - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
If a contour has less than this number of points, we don't split it, and return it as-is
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
Only includes squares that have at lesat this number of voxels
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
 
getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
The minimum number of voxels that must exist in a connected-component to be included.
getMinNumPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
 
getMinNumPoints() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
If an object has fewer points than before being fitted, we ignore
getMinNumSlices() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
getMinNumZSlices() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
 
getMinorAxisAngle() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
getMinorAxisSlope() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
getMinOverlap() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
 
getMinRadius() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
 
getMinRadius() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
 
getMinRadScaleEnd() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
getMinRadScaleStart() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
getMinRatio() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
getMinRatioPointsInsideRegion() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
 
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
 
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
 
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds
 
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
 
getMinSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
getMinusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
 
getMinVal() - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
getMinVolume() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
 
getMinVolume() - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
 
getMinVolumeConnectedComponent() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
 
getMinX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Minimum X coordinate inclusive
getMinXYRes() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
 
getMinY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Minimum Y coordinate inclusive
getMinZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Minimum Z coordinate inclusive
getModelDirectory() - Method in class org.anchoranalysis.core.log.CommonContext
Directory where machine-learning models can be found
getModelDirectory() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
getModelDirectory() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
 
getModelDirectory() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
getModelDirectory() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
An input-directory in which models are stored.
getModelDirectory() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
 
getModelPool() - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
 
getMultipleComparer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
getMultiplyBy() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
getName() - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
getName() - Method in class org.anchoranalysis.bean.NamedBean
The name associated with item
getName() - Method in class org.anchoranalysis.bean.shared.path.RootPath
 
getName() - Method in interface org.anchoranalysis.core.identifier.name.NameValue
The associated name
getName() - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
 
getName() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
 
getName() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
An optional-name.
getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
 
getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
 
getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
 
getName() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
A unique name associated with the path
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
 
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
 
getName() - Method in class org.anchoranalysis.mpp.mark.Mark
 
getName() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
getName() - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
getName() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
getName() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
getName() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
getName() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
 
getName() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
 
getName() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
 
getName() - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
A name to describe the adjacent file
getName() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
The name of the appended entity
getName(S) - Method in interface org.anchoranalysis.bean.permute.ApplyPermutations.NameGetter
 
getNamedFilePathCollection() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsInitParams
 
getNamedKeyValueParamsCollection() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsInitParams
 
getNameLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
 
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
 
getNamer() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
Assigns each input a unique compact name.
getNameRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
getNames() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
 
getNames() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
getNameValueSet() - Method in class org.anchoranalysis.overlay.OverlayProperties
 
getNavigateHigherDirs() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
Search x number directories higher than file
getNoProposalReason() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
 
getNumberChannels() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
 
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.Stack
 
getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
getNumberChannels() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
 
getNumberChannels() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
 
getNumberColors() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
 
getNumberDilations() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
 
getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
 
getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
 
getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
 
getNumberFrames() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
 
getNumberFrames() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
 
getNumberGPUProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
How many GPU processors to use when this is possible as a substitute for a CPU processor
getNumberKernels() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
getNumberLoopPoints() - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
 
getNumberPoints() - Method in class org.anchoranalysis.plot.index.LinePlot
 
getNumberSeries() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
getNumberSlices() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
 
getNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
How many directories to include in the name.
getNumBins() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The number of bins in each histogram for a cell
getNumCols() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
getNumColsUsed() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
 
getNumDecimalPlaces() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
getNumDim() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
getNumLeadingZeros() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
 
getNumLevelsGrouping() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
getNumMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
 
getNumRep() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
 
getNumRep() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
 
getNumRows() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
getNumRowsUsed() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
 
getObject() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
The found object
getObject() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
 
getObject() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
 
getObject() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
 
getObject() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
 
getObject() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
 
getObject1() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
 
getObject2() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
 
getObjectMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
Used to match each intermediary-object to a final-object
getObjects() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
 
getObjects() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
 
getObjects() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
 
getObjects() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
 
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
The objects for whom a level is calculated
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
 
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
 
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
 
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
 
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
 
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
 
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
 
getObjects() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
Objects to draw on a background
getObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
 
getObjects() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
The objects in the collection.
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
 
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
 
getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
 
getObjects() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
getObjects() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
 
getObjects() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not when outputting object-collections
getObjects() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
getObjects() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
getObjects1() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
First collection with items to be merged
getObjects2() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
Second collection with items to be merged
getObjectsBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
 
getObjectsContainer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
 
getObjectsElse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
 
getObjectsGreater() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
 
getObjectsGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
 
getObjectsGrouped() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
 
getObjectsLesser() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
 
getObjectsRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
 
getObjectsRejected() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
 
getObjectsSave() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
Saves all objects that are inputs to the merge, outputs from the merge, or intermediate merges along the way
getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
 
getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
 
getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
 
getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
 
getObjectsSplitBy() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
 
getObjectsTarget() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
 
getOffByte() - Method in class org.anchoranalysis.image.core.mask.Mask
 
getOffByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
The byte representation of the value for OFF
getOffInt() - Method in class org.anchoranalysis.image.core.mask.Mask
 
getOffInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
The integer representation of the value for OFF
getOnByte() - Method in class org.anchoranalysis.image.core.mask.Mask
 
getOnByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
The byte representation of the value for ON
getOnInt() - Method in class org.anchoranalysis.image.core.mask.Mask
 
getOnInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
The integer representation of the value for ON
GetOperationFailedException - Exception in org.anchoranalysis.core.index
When a get operation fails for a particular key
GetOperationFailedException(int, String) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
 
GetOperationFailedException(int, Throwable) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
 
GetOperationFailedException(Exception) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
 
GetOperationFailedException(String, String) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
 
GetOperationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
 
getOptimization() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
The optimization-scheme that determines which configurations are accepted/rejected from one iteration to the next.
getOptional(String) - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
Retrieves the item if it exists, or returns empty() if it doesn't exist.
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
 
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
 
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
 
getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
 
getOptional(String) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
 
getOptional(String) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
 
getOptional(String) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequence
 
getOptional(String) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
 
getOptional(String) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapTimeSequenceAsStack
 
getOptionList() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
getOptions() - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
 
getOptions() - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
 
getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCreate(Class<?>) - Method in class org.anchoranalysis.core.identifier.provider.store.SharedObjects
Gets an existing store, or creates a new one
getOrCreateNew(K) - Method in class org.anchoranalysis.core.identifier.name.MapCreate
 
getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
getOrientationProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
 
getOrientationXYProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
getOriginal() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
Original unscaled element before any operations
getOrNull(U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
Gets an existing result for the current params from the cache.
getOutlineColor() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
The color of the outline
getOutlinePixelsRetriever() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
getOutlinePixelsRetrieverReverse() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
getOutlineProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
 
getOutlineWidth() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
 
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
The width of the outline (only relevant if outline==true
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
The width of the outline.
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
The width of the outline
getOutlineWidth() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
getOutlineWidth() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
getOutPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
Constructs a path as an output, replacing $1, $2 etc.
getOutPathPrefix() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
A directory in which to output the experiment-directory and files
getOutput() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
The output-manager that specifies how/where/which elements occur duing outputting.
getOutput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
 
getOutput() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
getOutputDirectory() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
A directory indicating where inputs can be located
getOutputDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.FilePathPrefixerContext
A directory indicating where inputs can be located
getOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not - highest level outputs
getOutputEnabled() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
getOutputEnabledDelta() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
Additions/subtractions of outputs for the experiment supplied by the user.
getOutputFolderPath() - Method in class org.anchoranalysis.io.output.outputter.Outputter
 
getOutputFolderPath() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
 
getOutputName() - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileBase
The name to use (without extension) for the text-file log
getOutputName() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
The output name for the features CSV.
getOutputName() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
 
getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
 
getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle
An identifier used in rules to determine if an output is enabled or not.
getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
 
getOutputName() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
 
getOutputName() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
 
getOutputName() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
getOutputNameStyle() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
 
getOutputNameStyle() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
 
getOutputPattern() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
 
getOutputRGBOutline() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
getOutputRGBOutlineFlattened() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
getOutputsDisabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
The names of the outputs that are disbled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
The names of the outputs that are enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.OutputManager
Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
Which outputs are enabled or not enabled.
getOutputStackProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
getOutputter() - Method in class org.anchoranalysis.experiment.task.InputBound
 
getOutputter() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
 
getOutputter() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
 
getOutputter() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
The outputter to be used for the sequence.
getOutputter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
An outputter that writes to the particular output-directory.
getOutputter() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
getOutputterFor(String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
groupIdentifierFor should always called at least once before getOutputManagerFor
getOutputWriteSettings() - Method in class org.anchoranalysis.io.output.bean.OutputManager
General settings (default file extensions, colors etc.) for outtping files.
getOutputWriteSettings() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
getOutside() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
Returned as a constant if a value lies otside the range
getOverlapRatioThreshold() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
getOverlapThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
The maximum size for merging.
getOverlays() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
getOverlays() - Method in class org.anchoranalysis.overlay.IndexableOverlays
 
getPadding() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
Padding placed on each side of the outputted image (if it's within the image)
getPaddingXY() - Method in class org.anchoranalysis.image.bean.spatial.Padding
Padding placed on each side of the outputted image (if it's within the image) in XY directions
getPaddingZ() - Method in class org.anchoranalysis.image.bean.spatial.Padding
Padding placed on each side of the outputted image (if it's within the image) in Z direction
getPair() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
 
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
 
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
Every combination of interactions between marks and the associated energy
getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
 
getPairCollection() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
getPairsFor(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
getPairTypeClass() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
getParametersExperiment() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
 
getParamMean() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
getParamPrefix() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
getParams() - Method in class org.anchoranalysis.feature.energy.EnergyStack
 
getParams() - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
 
getParams() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
getParams() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getParams() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
getParams() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
getParams() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
getParams() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
getParams() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
 
getParams() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
 
getParams() - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
getParams() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
 
getParams() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
getParams() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
Parameters used for calculating HOG
getParams() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
Parameters used for calculating HOG
getParamsOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
getParamsOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputParams
 
getParamsOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
getParamsRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputParams
 
getParamStdDev() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
getParent() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
getParentDirectoryCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
 
getParentFolder() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
getParentFolder() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
 
getParentOutputter() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
 
getPartition() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
 
getPath() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
Path to annotation
getPath() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
the path an object was not found at.
getPath() - Method in class org.anchoranalysis.bean.shared.path.RootPath
A path on a filesystem to the directory, that defines the root
getPath() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
The path
getPath() - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
 
getPath() - Method in class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
 
getPathAnnotation() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
 
getPathDefaultMarks() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
getPathLabel() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
Path to a CSV label file (comma-separated, with header, no quotes)
getPathParams() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
getPaths() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
All files need to be present
getPaths() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
 
getPayload() - Method in class org.anchoranalysis.core.graph.TypedEdge
The edge.
getPayload() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
 
getPenaltyValue() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
getPeriodTriggerBank() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
getPermutation() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
A permutation to apply.
getPermutations() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
A list of permutations to apply.
getPermuteProperty() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
 
getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
 
getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
getPixelsForPlane(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
getPlotBackgroundColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
getPlotGridlineColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
getPlusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
 
getPoints() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getPoints() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
 
getPoints() - Method in class org.anchoranalysis.spatial.Contour
 
getPointsFitter() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
 
getPointsFitter() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
Name of the PointsFitter to use.
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
 
getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
getPointsFitterSet() - Method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
 
getPointsFromOrientationProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
 
getPointsFromOrientationXYProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
getPointsProposer() - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
getPos() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
 
getPositionProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
 
getPositionProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
 
getPower() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
 
getPrefix() - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
A prefix that is placed before the name of every bean created
getPrefix() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
 
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
 
getPrefix() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
 
getPrefix() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
getPrefixer() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
The OutputManager associated with the experiment which Outputter uses.
getPrependColor() - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
 
getPrependString() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
 
getPrependString() - Method in class org.anchoranalysis.feature.bean.list.PrependName
 
getPrependString() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
 
getPrependString() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
 
getPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
 
getProbMapID() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
 
getProbMapSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getProbNeg() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
 
getProbPos() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
 
getProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
getProperty(String) - Method in class org.anchoranalysis.core.value.KeyValueParams
 
getProperty(String) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
getPropertyAsDouble(String) - Method in class org.anchoranalysis.core.value.KeyValueParams
 
getPropertyDefiner() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
 
getPropertyInitializer() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
 
getPropertyPath() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
Either a direct property of a bean e.g.
getProposal() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
getProposal() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getProposalSecondary() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
An optional additional marks-Energy that provides an additional explanation of proposed
getProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
 
getProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
 
getProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
 
getPxlPartMemo() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
 
getPxlPartMemo() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
 
getQuantile() - Method in class org.anchoranalysis.feature.bean.results.Quantile
The quantile.
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
 
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
 
getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
 
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
 
getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
 
getQuantileHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
 
getQuantileLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
 
getQuantileLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
 
getQuantileUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
 
getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
getRadiiProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
 
getRadiiProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
 
getRadius() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
 
getRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
getRadius() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
 
getRadius() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
 
getRadiusBound() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
 
getRadiusBound() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
 
getRadiusX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
getRadiusY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
getRadiusZ() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
getRandomNumberGenerator() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
getRangeAxisLimits() - Method in class org.anchoranalysis.plot.PlotInstance
 
getRangeC() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
 
getRangeT() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
 
getRangeZ() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
 
getRate() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
 
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Gets an unsigned-byte (represented as a byte) at the current buffer position.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Gets an unsigned-int (represented as an int) at the current buffer position.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Gets an unsigned-short (represented as a short) at the current buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Gets an unsigned-byte (represented as a byte) at a particular buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Gets an unsigned-int (represented as a int) at a particular buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Gets an unsigned-short (represented as a short) at a particular buffer position.
getReason() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
 
getReceive() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
 
getRecordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules
If defined, records output-names that are written / not-written during the experiment.
getRed() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
getRed() - Method in class org.anchoranalysis.core.color.RGBColor
 
getRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
getReduce() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
Method for reducing all pairs into a single value e.g.
getReduce() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
The algorithm for reducing the number of object-masks.
getReferencePoissonIntensity() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
getReferencesFeatureListCreator() - Method in class org.anchoranalysis.feature.bean.list.ReferencedFeatures
Ensures any feature-lists mentioned here are evaluated, before this list is created.
getReferencesFeatureListCreator() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
Makes sure a particular feature list creator is evaluated
getRegex() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
 
getRegex() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
Regular expression to match against string
getRegex() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
A regular-expression applied to the image file-path that matches three groups.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
 
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
Regular expression to use to match path with at least one group in it.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
 
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
The regular-expression to use for matching groups.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
 
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
If a path matches a regular expression it is removed.
getRegEx() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
getRegexAdjacent() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
This needs to be set if there is at least one adjacentChannel.
getRegExDir() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
If non-empty a regular-expression is applied to directories
getRegExFile() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
If non-empty a regular-expression is applied to files
getRegion() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
 
getRegion() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
 
getRegionID() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
getRegionID() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
 
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
 
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
 
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.FeatureMarkRegion
 
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
 
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
 
getRegionID() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
getRegionID() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
 
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
 
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
getRegionMap() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
 
getRegionMap() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
 
getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
 
getRegionMap() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
getRegionMembership() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
 
getRejectionReason() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
 
getRelation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
 
getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
Relation to threshold
getRelation() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
getRelation() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
 
getRelation() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
 
getRelation() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
getRemainder() - Method in class org.anchoranalysis.core.system.path.SplitPath
 
getRepeat() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
getRepeats() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
Total number of births
getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
 
getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
What to replace in the path
getReplacement() - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
The replacement string used to determine the file
getRequireArguments() - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
The conditions that must be fulfilled
getRequireArguments() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
 
getResizeTo() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
If set, each channel is scaled to a specific size before the mean is calculated (useful for combining different sized images)
getResizeTo() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
The input-image is rescaled to this width/height before calculating HOG descriptors
getResizeTo() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
The input is rescaled to this width/height before calculating HOG descriptors
getResolution() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
 
getResolutionOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
getResolutionOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution
 
getResolutionOptional() - Method in class org.anchoranalysis.image.feature.histogram.FeatureInputHistogram
 
getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
 
getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
getResolutionRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution
 
getRestrictTo() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
If set, the inversion only occurs on a particular region of the mask, as determined by this mask
getResults() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
 
getResultsVector() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
 
getResX() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
getResY() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
getResZ() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
getReverse() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
 
getRGB() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
getRGB() - Method in class org.anchoranalysis.core.color.RGBColor
 
getRight() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
Objects on right-side of the comparison
getRoot() - Method in class org.anchoranalysis.core.system.path.SplitPath
 
getRoot() - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
 
getRoot() - Method in class org.anchoranalysis.test.TestLoader
 
getRoot1() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
 
getRoot2() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
 
getRootFolder() - Method in class org.anchoranalysis.io.manifest.Manifest
 
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
 
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
 
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
 
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
 
getRootName() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
If non-empty then a rooted filesystem is used with this root
getRootName() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
Root-name assuming multi-rooted strucutre
getRootName() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
getRootNameForStructure() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
If rootInStructure==true, the rootName is placed in the folder structure.
getRootPath() - Method in class org.anchoranalysis.plugin.io.manifest.DeserializedManifest
 
getRotationAngle() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
 
getRotationAngle() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
 
getRotationBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
 
getRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
getRotationX() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
 
getRotationY() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
 
getRotationZ() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
 
getRotMatrix() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
getRow() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
 
getRow(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
 
getRowForListIndex(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
 
getRowSource() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
 
getSampleEvery() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
 
getScalarProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
 
getScalarProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
 
getScale() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
Standard-Deviation
getScale() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
Whether to increase or reduce the size of the images
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
 
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
Determines how much to scale by
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
 
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
 
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
 
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
getScaleCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
 
getScaleFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
 
getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
Sets the min by multiplying the quantileLower by this constant.
getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
getScaleRadii() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
Sets the max by multiplying the quantileUpper by this constant.
getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
getScore() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
getScoreProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
getScoreThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
Bounding boxes with scores above this threshold are removed
getSearchObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
 
getSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
 
getSecond() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
getSecond() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
Output-names in the second-level (for all first level output-names)
getSecond() - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
Second transformation from U to T
getSecondary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
 
getSegment() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
 
getSegment() - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
 
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
Segmentation algorithm
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
 
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
 
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
The segmentation procedure.
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
 
getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
 
getSegment() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
The segmentation algorithm
getSegment() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
How to perform the segmentation.
getSegment() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
The segmentation algorithm that is applied as an input to non-maxima suppression.
getSegmentStack() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
 
getSelect() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
Either "merged" or "first" or "second" indicating which feature to delegate from
getSelectChannels() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
Selects which channels are included, optionally renaming.
getSemiMajorAxis() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
getSemiMinorAxis() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
 
getSeperator() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
 
getSeperator() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
getSequence() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence
Where the sequence starts
getSequence() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
First number range that is appended
getSequence() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
 
getSequenceAdditional() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
Another number range that is appended
getSequenceType() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
 
getSequenceType() - Method in class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
A sequence-type to describe the different filenames outputted in the directory.
getSeriesColors() - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
 
getSeriesNameFor(int) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
getSet() - Method in class org.anchoranalysis.feature.shared.SharedFeatureSet
 
getSetPoints() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
getSettings() - Method in class org.anchoranalysis.io.output.outputter.Outputter
 
getSettings() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
General settings for writing outputs.
getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
 
getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
 
getSharedFeatureSet() - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
 
getSharedObjects() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
 
getSharedObjects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
getSharedState() - Method in class org.anchoranalysis.experiment.task.InputBound
 
getSharedState() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
 
getShellRad() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
 
getShellRad() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
 
getShellRad() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
getShellRad() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
getShellRad() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
getShellRad() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
 
getShellRad() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
getShift() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
 
getShortTitle() - Method in class org.anchoranalysis.plot.bean.Plot
A shortened version of Plot.getTitle().
getShowOngoingJobsLessThan() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
getSigma() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
 
getSigma() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
 
getSimplePairCollection() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
getSimplePairCollectionID() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
getSingle() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
 
getSize() - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
 
getSize() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
getSize() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
Size of the image produced showing a plot of the histogram
getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
Size of all created thumbnails
getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
 
getSize() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
getSize() - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange
 
getSizeHalf() - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
 
getSkipFirstTrim() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
 
getSkipFirstTrim() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
getSkipNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
Initially skip this number of directories before including them in the description.
getSlice() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
 
getSlice(int) - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
 
getSlice(int) - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
 
getSliceEnd() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
 
getSliceFirst() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
First slice.
getSliceID() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
Index of slice to use, or -1 to use all slices
getSliceIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
Which slice to use from mask
getSliceLast() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
Last slice.
getSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
 
getSliceStart() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
 
getSmoothingFactor() - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
 
getSource() - Method in class org.anchoranalysis.bean.shared.StringMapItem
 
getSource() - Method in class org.anchoranalysis.image.core.object.MatchedObject
The source object (which is matched against others)
getSource() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
 
getSource() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
 
getSource() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
Source of feature-values to be exported
getSource() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.DualVoxelizedMarks
 
getSource() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
 
getSourceFolderPath() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
getSplitDescriptiveNameRegex() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
getSplitProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
getSquareSize() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
 
getStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
 
getStack() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
getStack() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
getStack() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
 
getStack() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
Provides a stack.
getStack() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
The stack to segment
getStack() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
The stack that is the background for our objects
getStackEnergy() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
Optionally specifies an energy-stack to be associated with every calculation input.
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks)
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
 
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
getStackEnergy() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
 
getStackID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
 
getStackName() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
If defined, processing only occurs the stack with this specific stack and index.
getStackNameVisualOriginal() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
 
getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
Specifies the ID of an existing stack.
getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
 
getStackReader() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
 
getStackReader() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
getStackReader() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
 
getStackReader() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
getStackReader() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
 
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
 
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
 
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
 
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
 
getStackReader() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
The raster-reader for reading the main file
getStackReaderAdjacent() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
The raster-reader to use for opening any adjacent-channels
getStackReaderAppend() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
The raster-reader for reading any appended files
getStackReaderHigh() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
getStackReaderInput() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
getStackReaderLow() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
getStackReaderMiddle() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
getStacksOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not when outputting stacks
getStacksOutputEnabled() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
getStackStore() - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
 
getStart() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
The index to begin iteration from
getStartIndex() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
getStartingIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
The first intensity-value to consider as a valid object (e.g.
getStartPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
getState() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
 
getStateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
getStrategy() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
 
getStrategy() - Method in class org.anchoranalysis.feature.session.strategy.replace.bind.BoundReplaceStrategy
 
getStrategy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
 
getSubdirectory() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
If non-empty than an additional subdirectory is appended as a suffix ${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
getSubDirectory() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
 
getSubdirectoryName() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
The name of a subdirectory in the current context to write to, or if empty, files are written into the current directory context.
getSubtractConstant() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
getSubtractRadii() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
getSuffix() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
 
getSum() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
The running sum
getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
 
getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
 
getSummarizerElse() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
Used for summary if count(elements) <= countThreshold
getSummarizerGreaterThan() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
Used for summary if count(elements) > countThreshold
getTarget() - Method in class org.anchoranalysis.bean.shared.StringMapItem
 
getTask() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
 
getTask() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
 
getTask() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
getTask() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
getTask() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
getTask() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
getTaskName() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
A name to describe the ongoing task
getTaskProcessor() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
What task is associated with the experiment, and how it is processed.
getTemperature() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
getTemperature() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
getTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
getTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
GetterFromIndex<T> - Interface in org.anchoranalysis.core.index
 
getTermination() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
 
getThreshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
 
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
 
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
 
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
 
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
 
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
 
getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold
Only considers values greater or equal to the threshold
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
 
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
 
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
 
getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
 
getThreshold() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
 
getThresholder() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
 
getThresholder() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
The thresholder that will convert a channel into a binary-channel
getThresholdHigh() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
getThresholdLow() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
getThumbnail() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
Generates a thumbnail representation of one or more objects combine, as form a single input
getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
Method to generate a thumbnail for images
getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
 
getThumbnailBatch() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
 
getTime() - Method in class org.anchoranalysis.experiment.task.processor.JobState
 
getTimeAnnotationLastUpdated() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
Number of seconds since the UNIX epoch
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
 
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
 
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
 
getTimeIndexGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
getTimes() - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
 
getTitle() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
 
getTitle() - Method in class org.anchoranalysis.plot.bean.Plot
The full title of the plot.
getTitle() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
 
getTo() - Method in class org.anchoranalysis.core.graph.TypedEdge
The vertex the edge joins to.
getToleranceLog10() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
 
getTotal() - Method in class org.anchoranalysis.feature.energy.EnergyTotal
 
getTotal() - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
 
getTotalCount() - Method in class org.anchoranalysis.math.histogram.Histogram
 
getTotalNumberTasks() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
getTransformer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
 
getTransformer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
 
getTransformer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
 
getTransformerKernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
 
getTransformerMarks() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
 
getTransformerPrimary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
 
getTransformerSecondary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
 
getTransformerStateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
 
getTriggerTerminationCondition() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
getTrimTrailingDirectory() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
 
getTrimTrailingDirectory() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
getType() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
Identifies the type of entity.
getUnconvertedVoxelAt(int, Point3i) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
getUniqueLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
Label that uniquely identifies the ID (for machine purposes)
getUnit() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
 
getUnit() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
 
getUnitConverterOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
 
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
 
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
 
getUnitType() - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
 
getUnitType() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
 
getUnitTypeFrom() - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
 
getUnitTypeTo() - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
 
getUnitValueDistance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
 
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
Gets an unsigned-byte (represented as a int) at the current buffer position.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
 
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Gets an unsigned-int (represented as a long) at the current buffer position.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
 
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
Gets an unsigned-byte (represented as a int) at a particular buffer position.
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
 
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Gets an unsigned-int (represented as a long) at a particular buffer position.
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
 
getUnsignedByte() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
 
getUnsignedInt() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
 
getUnsignedShort() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
 
getUsageFooter() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
 
getUsageHeader() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
 
getUserFriendlyLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
Descriptive user-friendly label displayed via GUI
getValue() - Method in class org.anchoranalysis.bean.NamedBean
 
getValue() - Method in interface org.anchoranalysis.core.identifier.name.NameValue
The associated value
getValue() - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
 
getValue() - Method in class org.anchoranalysis.core.value.TypedValue
 
getValue() - Method in class org.anchoranalysis.feature.bean.operator.Constant
 
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
 
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
 
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
 
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
 
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
 
getValue() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
The value.
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
 
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
 
getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
 
getValue() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
 
getValue() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
getValue() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
 
getValue() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
 
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
 
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
 
getValue() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
 
getValue() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
 
getValue() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
 
getValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
 
getValueIfEmpty() - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
The value to return iff exceptionifEmpty is false
getValueIfTooFewVoxels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate moments
getValueNoObject() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
 
getValueNoObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
 
getValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
 
getValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
The values of the string-set
getVersion() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
 
getVersionFooter() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
 
getVertex() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
 
getVerticalAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
 
getVisitScheduler() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
getVoxelDataType() - Method in class org.anchoranalysis.image.core.channel.Channel
 
getVoxelDataType() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
getVoxels() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
 
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
 
getVoxelsConverter() - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached
 
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
 
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
 
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
 
getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter
 
getWeight() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
 
getWeight() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
 
getWeightBackground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
getWeightedKernelFactory(int) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
getWeightForeground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
getWeightItem1Greater() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
 
getWeightItem2Greater() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
 
getWeightNegative() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
 
getWeightNegative() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
getWeightNegative() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
 
getWeightPositive() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
 
getWeightPositive() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
getWeightPositive() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
 
getWeightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
 
getWhenDetailed() - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
Logger to use when detailed-logging is on
getWhenEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
getWhenNot() - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
Logger to use when detailed-logging is off
getWhenNotEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
getWhenOneOrThreeChannels() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
Writer employed if a stack is a one or three-channeled image, that is not 3D, and not RGB.
getWhenRGB() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
Writer employed if a stack is a three-channeled RGB image and is not 3D.
getWidth() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
 
getWidth() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
Width (what the difference is divided by)
getWidthFactor() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
 
getWindowSize() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
 
getWindowSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The window-size as per OpenCV implementation.
getWithin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
Returned as a constant if a value lies within the range
getWithinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
Constant to return if value lies within the range
getWithinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
Constant to return if value lies within the range
getWriter() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
 
getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
Default writer, if a more specific writer is not specified for a condition.
getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
 
getWriterAlways2D() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
Writer to use if it is guaranteed that the image will always be 2D.
getWriterElse() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
Otherwise the writer to use.
getWriterInstance(Class<?>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
Gets a writer-instance for a particular writerParentClass.
getWriters() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
getWriters() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
The writers associated with this output-manager.
getX() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
getX() - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
 
getXMax(Point3i, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
 
getXMin(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
 
getXmlAggregatedGroup() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
The name of the XML file outputted with aggregated values for each group, if enabled.
getXMLConfiguration() - Method in class org.anchoranalysis.experiment.bean.Experiment
 
getY() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
getY() - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
 
getYAxisLowerMargin() - Method in class org.anchoranalysis.plot.index.LinePlot
 
getYAxisUpperMargin() - Method in class org.anchoranalysis.plot.index.LinePlot
 
getYMax(Point3i, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
 
getYMin(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
 
getYVal(T, int) - Method in interface org.anchoranalysis.plot.index.LinePlot.YValGetter
 
getYValGetter() - Method in class org.anchoranalysis.plot.index.BarPlot
 
getYValGetter() - Method in class org.anchoranalysis.plot.index.LinePlot
 
getZ() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
getZAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
 
getZSliceGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
getZSliceNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
 
getZSliceNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
getZSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
 
GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark
 
GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
 
GradientBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
 
GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
 
GradientBaseAddSum() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
 
gradientCalculation() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
Extracts the gradient in the direction of a particular axis (identified by an index)
GradientForAxis() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
 
GradientMagnitude - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMagnitude() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMagnitude
 
GradientMeanForAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMeanForAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
 
GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
Gradient in x and y axes
GradientXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
 
GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge
 
GraphLogger(DescribeGraph, Logger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.GraphLogger
 
GraphWithoutPayload<V> - Class in org.anchoranalysis.core.graph
A graph, either directed or undirected, where edges contain no payload.
GraphWithoutPayload(boolean) - Constructor for class org.anchoranalysis.core.graph.GraphWithoutPayload
Creates the graph.
GraphWithPayload<V,​P> - Class in org.anchoranalysis.core.graph
A graph, either directed or undirected, with edges containing a payload of type E.
GraphWithPayload(boolean) - Constructor for class org.anchoranalysis.core.graph.GraphWithPayload
Creates the graph.
GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
 
GrayscaleReconstruction2DIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ
 
GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
 
GrayscaleReconstructionByErosion() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion
 
GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
 
GrayscaleReconstructionRobinson() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
 
greaterEqualThan(VarianceCalculator) - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
 
GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater than objectsLesser
GreaterIntersectionWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
 
GreaterThan - Class in org.anchoranalysis.math.relation
 
GreaterThan() - Constructor for class org.anchoranalysis.math.relation.GreaterThan
 
GreaterThanBean - Class in org.anchoranalysis.bean.shared.relation
 
GreaterThanBean() - Constructor for class org.anchoranalysis.bean.shared.relation.GreaterThanBean
 
GreaterThanEqualTo - Class in org.anchoranalysis.math.relation
 
GreaterThanEqualTo() - Constructor for class org.anchoranalysis.math.relation.GreaterThanEqualTo
 
GreaterThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
 
GreaterThanEqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
 
GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the threshold
GreaterThanThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
 
GreatestAreaSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
 
GreatestAreaSlice() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
 
greedyMatch() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
Find a valid matching by greedily selecting among zero-cost matchings.
green() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label
A set of annotation labels partitoned into their unique groups
GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
 
groupedLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
 
GroupedMeanChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.grouped.raster
Creates a an aggregated-image for each group, where each voxel-value is the mean voxel-value across the group.
GroupedMeanChannelTask() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
 
GroupedSharedState<S,​T> - Class in org.anchoranalysis.plugin.image.task.grouped
Commonality between shared state for gouped export tasks
GroupedSharedState(Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState
 
GroupedStackBase<S,​T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped
Base class for stacks (usually each channel from an image) that are somehow grouped-together.
GroupedStackBase() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
 
GroupFiles - Class in org.anchoranalysis.plugin.io.bean.groupfiles
An input-manager that can group together files to form stacks or time-series based on finding patterns in the file path (via regular expressions)
GroupFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
 
groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
 
GroupingRoot - Annotation Type in org.anchoranalysis.bean.annotation
Indicates that a set of definitions of classes can be collectively grouped using this class.
GroupMapByName<S,​T> - Class in org.anchoranalysis.plugin.image.task.grouped
Adds items to aggregate structures identified uniquely by a name, and allows these items to be later outputted.
GroupMapByName(String, String, Supplier<T>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
Creates a group-map.
groupNameSet() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.IndexedCSVRows
 
GroupWriter - Class in org.anchoranalysis.feature.io.results.group
Writes outputs pertaining to groups to the filesystem.
GroupWriter(ResultsWriterMetadata) - Constructor for class org.anchoranalysis.feature.io.results.group.GroupWriter
 
growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Grows buffer of the object-mask in positive and negative directions by a certain amount.
growBy(int) - Method in class org.anchoranalysis.spatial.Extent
 
growBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
 
growBy(Tuple3i, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
growToZ(int) - Method in interface org.anchoranalysis.image.core.object.seed.Seed
 
growToZ(int) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
growToZ(int) - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
 
growToZ(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
 
guaranteedImageAttributes() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
 
guaranteedImageAttributes() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
 
guaranteedImageAttributes() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
 
GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
Guesses dimensions from the input-image if it exists.
GuessDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions
 

H

has(int) - Method in interface org.anchoranalysis.core.color.ColorIndex
 
has(int) - Method in class org.anchoranalysis.core.color.ColorIndexModulo
 
has(int) - Method in class org.anchoranalysis.core.color.ColorList
 
has(int) - Method in class org.anchoranalysis.core.color.SingleColor
 
has(K) - Method in class org.anchoranalysis.core.cache.LRUCache
 
has(T) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
Checks whether the cache contains a particular input already.
hasAboveZero() - Method in class org.anchoranalysis.math.histogram.Histogram
 
hasAllRequiredArguments(boolean) - Method in class org.anchoranalysis.experiment.bean.require.RequireArguments
 
hasAllRequiredArguments(boolean) - Method in class org.anchoranalysis.experiment.bean.require.RequireDebugMode
 
hasArray() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Whether the buffer has an array?
hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
If there is at least one disabled output.
hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
If there is at least one disabled output.
hasAtLeastOneEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
If there is at least one enabled output.
hasAtLeastOneMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
hasBeenInit() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
 
hasBeenInitialized() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
 
hasCachedCalculation() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
 
hasChannel(String) - Method in class org.anchoranalysis.plugin.image.task.channel.ChannelGetterForTimepoint
 
hasColorGetter() - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
 
hasEqualXAndY() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
HasFriendlyErrorMessage - Interface in org.anchoranalysis.core.exception.friendly
Methods for extracting a user-friendly error description
hashCode() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
 
hashCode() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
 
hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
 
hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
 
hashCode() - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
 
hashCode() - Method in class org.anchoranalysis.bean.shared.path.RootPath
 
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
 
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
 
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
 
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
 
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
 
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
 
hashCode() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
hashCode() - Method in class org.anchoranalysis.core.color.RGBColor
 
hashCode() - Method in class org.anchoranalysis.core.concurrency.WithPriority
 
hashCode() - Method in class org.anchoranalysis.core.graph.TypedEdge
 
hashCode() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
 
hashCode() - Method in class org.anchoranalysis.core.index.Indexable
 
hashCode() - Method in class org.anchoranalysis.core.log.CommonContext
 
hashCode() - Method in class org.anchoranalysis.core.system.path.SplitPath
 
hashCode() - Method in class org.anchoranalysis.core.value.TypedValue
 
hashCode() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
 
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
 
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
 
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
 
hashCode() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
 
hashCode() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
 
hashCode() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
 
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputNull
 
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
 
hashCode() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
 
hashCode() - Method in class org.anchoranalysis.feature.io.name.CombinedName
 
hashCode() - Method in class org.anchoranalysis.feature.io.name.SimpleName
 
hashCode() - Method in class org.anchoranalysis.feature.results.ResultsVector
 
hashCode() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
hashCode() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
 
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
 
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
 
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
 
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
 
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
 
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
 
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
 
hashCode() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
hashCode() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
hashCode() - Method in class org.anchoranalysis.image.core.mask.Mask
 
hashCode() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
 
hashCode() - Method in class org.anchoranalysis.image.core.object.MatchedObject
 
hashCode() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
hashCode() - Method in class org.anchoranalysis.image.core.orientation.Orientation
 
hashCode() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
hashCode() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
hashCode() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
hashCode() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
hashCode() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
hashCode() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
 
hashCode() - Method in class org.anchoranalysis.image.core.stack.Stack
 
hashCode() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
 
hashCode() - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
 
hashCode() - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
 
hashCode() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
 
hashCode() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
hashCode() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
 
hashCode() - Method in class org.anchoranalysis.image.feature.stack.FeatureInputStack
 
hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
 
hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
 
hashCode() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
 
hashCode() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
 
hashCode() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
 
hashCode() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
hashCode() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
 
hashCode() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
 
hashCode() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
 
hashCode() - Method in class org.anchoranalysis.io.manifest.file.FileType
 
hashCode() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
 
hashCode() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
 
hashCode() - Method in class org.anchoranalysis.io.output.outputter.Outputter
 
hashCode() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
 
hashCode() - Method in class org.anchoranalysis.launcher.config.HelpConfig
 
hashCode() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
 
hashCode() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
 
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
 
hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
 
hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
 
hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
 
hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
 
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
 
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
 
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
 
hashCode() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
hashCode() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
hashCode() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
 
hashCode() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
 
hashCode() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
 
hashCode() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
 
hashCode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
hashCode() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
 
hashCode() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
 
hashCode() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
hashCode() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
 
hashCode() - Method in class org.anchoranalysis.overlay.IndexableOverlays
 
hashCode() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
 
hashCode() - Method in class org.anchoranalysis.overlay.Overlay
 
hashCode() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
 
hashCode() - Method in class org.anchoranalysis.plot.AxisLimits
 
hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
 
hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
 
hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
 
hashCode() - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
 
hashCode() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
 
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
 
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
 
hashCode() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
 
hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
 
hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
 
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
 
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
 
hashCode() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
 
hashCode() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
 
hashCode() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
 
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
 
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
 
hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
 
hashCode() - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
hashCode() - Method in class org.anchoranalysis.spatial.Extent
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Point2d
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Point2f
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Point2i
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Point3d
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Point3f
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Point3i
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
hashCode() - Method in class org.anchoranalysis.spatial.point.Vector3d
 
hashCode() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
 
hasIdenticalXY() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
 
hasInputFilterExtensions() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
hasIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
hasIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Determines whether there are any intersecting voxels on two object-masks.
hasIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects
Determines whether there are any intersecting voxels on two object-masks.
hasKey(U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
 
hasLastDivider() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
hasMatch(String) - Method in class org.anchoranalysis.bean.shared.regex.RegEx
Returns a boolean whether the regular-expression successfully matches a string or not
hasMoreThanOneSlice() - Method in class org.anchoranalysis.image.core.stack.Stack
Does the stack have more than one slice in the z-dimension?
hasNecessaryExtents() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
 
hasNext() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
 
hasNext() - Method in interface org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement.TableCreator
 
hasNext() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
 
hasNoCombinableNestedExceptions() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
Are there nested-exceptions (according to our traversal rules) that are combinable?
hasNoNulls() - Method in class org.anchoranalysis.feature.results.ResultsVector
 
hasOffVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
hasOneSlice() - Method in class org.anchoranalysis.feature.energy.EnergyStack
Does exactly one z-slice exist in the energy stack?
hasOnVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
hasOption(String) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter
Identical to CommandLine.hasOption(java.lang.String).
hasPoint(Point3f) - Method in class org.anchoranalysis.spatial.Contour
 
hasProperty(String) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Whether there are elements between the current position and the limit Buffer.hasRemaining().
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
Are there voxels remaining in a buffer?
hasSingleFeature() - Method in class org.anchoranalysis.feature.session.SequentialSession
 
hasTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
HasTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
A simple scheme for counting the touching voxels.
HasTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
Is the execution-time of the task per-input expected to be very quick to execute?
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.task.HelloWorld
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.task.Task
Is the execution-time of the task per-input expected to be very quick to execute?
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
 
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
 
hasWrittenHeaders() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
 
head() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
 
headers() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
 
headers() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
 
headers() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
HelloWorld<S extends InputFromManager> - Class in org.anchoranalysis.experiment.bean.task
A dummy task that simply writes a message to all log files, specifically: 1.
HelloWorld() - Constructor for class org.anchoranalysis.experiment.bean.task.HelloWorld
 
help() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
Config for displaying help message
HelpConfig - Class in org.anchoranalysis.launcher.config
 
HelpConfig(String, String) - Constructor for class org.anchoranalysis.launcher.config.HelpConfig
 
HelperFriendlyExceptions - Class in org.anchoranalysis.bean.xml.error
Converts certain exceptions that occur from XML-Parsing into a friendly form to display to the user
HelperListUtilities - Class in org.anchoranalysis.bean.xml.factory
Utilities for manipulating list of beans
hexString() - Method in class org.anchoranalysis.core.color.RGBColor
 
higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
 
higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
 
higherCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
Whether the count is greater than a particular threshold.
highestConfidence() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
 
histogram() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
 
histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
 
histogram() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
histogram(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
 
Histogram - Class in org.anchoranalysis.math.histogram
 
Histogram(int) - Constructor for class org.anchoranalysis.math.histogram.Histogram
 
Histogram(int, int) - Constructor for class org.anchoranalysis.math.histogram.Histogram
 
Histogram.BinConsumer - Interface in org.anchoranalysis.math.histogram
Consumers a bin and corresponding count.
HistogramFactory - Class in org.anchoranalysis.image.voxel.statistics
 
HistogramFixture - Class in org.anchoranalysis.test.feature.plugins
 
HistogramFromObjectsFactory - Class in org.anchoranalysis.image.core.object
 
HistogramProvider - Class in org.anchoranalysis.image.bean.provider
 
HistogramProvider() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProvider
 
HistogramProviderUnary - Class in org.anchoranalysis.image.bean.provider
 
HistogramProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
 
histograms() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
HISTOGRAMS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories
Where collections of histograms are typically placed in a define-experiment output
HistogramStatistics - Class in org.anchoranalysis.math.histogram
Further statistics that can be derived from a histogram in addition to those callable directly from the Histogram class
HistogramThresholder - Class in org.anchoranalysis.plugin.image.intensity
 
HOGDescriptor - Class in org.anchoranalysis.plugin.opencv.bean.feature
Creates the entire HOG descriptor for an image.
HOGDescriptor() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
 
HOGFeature - Class in org.anchoranalysis.plugin.opencv.bean.feature
One part of a Histogram of Oriented Gradients descriptor, as applied to an image stack.
HOGFeature() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
 
HOGFeature(SizeXY, int) - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
 
HOGParameters - Class in org.anchoranalysis.plugin.opencv.bean.feature
Parameters for calculating a HOG Descriptor covering window-size, block-size etc.
HOGParameters() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
 
HomeSubdirectory - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
 
HomeSubdirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
 
HorizontalCalculationCache<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.cache.horizontal
Caches CachedCalculations that occur repeatedly across many features, and store similar child caches.
HorizontalCalculationCacheFactory - Class in org.anchoranalysis.feature.session.cache.horizontal
 
HorizontalCalculationCacheFactory() - Constructor for class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCacheFactory
 
HorizontalFeatureCache<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.cache.horizontal
Caches repeated-calls to the same feature, or references to a feature by an ID-value
HorizontalFeatureCacheFactory - Class in org.anchoranalysis.feature.session.cache.horizontal
 
HorizontalFeatureCacheFactory() - Constructor for class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCacheFactory
 
HSB - Class in org.anchoranalysis.bean.shared.color.scheme
 
HSB() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.HSB
 
HungarianAlgorithm - Class in org.anchoranalysis.math.optimization
An implementation of the Hungarian algorithm for solving the assignment problem.
HungarianAlgorithm(double[][]) - Constructor for class org.anchoranalysis.math.optimization.HungarianAlgorithm
Construct an instance of the algorithm.

I

idAndIncrement() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
Identifiable - Interface in org.anchoranalysis.overlay.identifier
 
IdentifiablePair<T extends Identifiable> - Class in org.anchoranalysis.mpp.pair
Pair of marks
IdentifiablePair(T, T) - Constructor for class org.anchoranalysis.mpp.pair.IdentifiablePair
 
identifier() - Method in class org.anchoranalysis.mpp.mark.Mark
 
identifier() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifier
Creates an identifier for the experiment
identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
 
identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
 
IdentifierByProperty - Class in org.anchoranalysis.image.core.object.properties
 
IdentifierByProperty(String) - Constructor for class org.anchoranalysis.image.core.object.properties.IdentifierByProperty
 
IdentifierFromMark - Class in org.anchoranalysis.mpp.mark
 
IdentifierFromMark() - Constructor for class org.anchoranalysis.mpp.mark.IdentifierFromMark
 
IdentifierFromOverlay - Class in org.anchoranalysis.overlay.identifier
 
IdentifierFromOverlay() - Constructor for class org.anchoranalysis.overlay.identifier.IdentifierFromOverlay
 
IdentifierGetter<T> - Interface in org.anchoranalysis.core.identifier.getter
 
IdentifierModulo<T> - Class in org.anchoranalysis.core.identifier.getter
 
IdentifierModulo() - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifierModulo
 
IdentifierModulo(IdentifierGetter<T>, int) - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifierModulo
 
IdentifyByIteration<T> - Class in org.anchoranalysis.core.identifier.getter
 
IdentifyByIteration() - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifyByIteration
 
IdentifyDelegateToOverlays - Class in org.anchoranalysis.overlay.identifier
 
IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection) - Constructor for class org.anchoranalysis.overlay.identifier.IdentifyDelegateToOverlays
 
IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection, boolean) - Constructor for class org.anchoranalysis.overlay.identifier.IdentifyDelegateToOverlays
 
IdentifyObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
Assigns a unique id number to each object.
IdentifyObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
 
Identity - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
Identity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
IdentityImposeValueRelationToHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
IdentityImposeValueRelationToHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
idFor(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
ID for a particular object
IfCondition<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.conditional
The result of featureCondition is compared to a threshold, and then either the underlying feature is calculated (positive case), or featureElse is (negative case)
IfCondition() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
 
IfConditionWithinRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
Calculates a value if a condition lies within a certain range, otherwise returns constants
IfConditionWithinRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
 
IfGreaterThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
Calculates a level from the first delegate and if greater than a threshold, recalculates from a second delegate.
IfGreaterThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
 
IfHighLow - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both masks, modifying {mask} with the result.
IfHighLow() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
 
IfKeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
IfKeyValueCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
 
IfLessThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
Calculates a level from the first delegate and if less than a threshold, recalculates from a second delegate.
IfLessThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
 
IfNotEmpty - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
The current mask is returned if it's non-empty (at least one ON voxel) otherwise maskElse is returned.
IfNotEmpty() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
 
IfObjectFilter - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
The current mask is returned if the mask (treated as an object) passed an object-filter, otherwise maskElse is returned.
IfObjectFilter() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
 
IfOutsideRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
Clips a value if it lies outside the range - instead returning particular constants if below or above an acceptable range
IfOutsideRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
 
IfParamEqual - Class in org.anchoranalysis.plugin.image.bean.object.provider
Multiplexes between two object-collection-providers depending on whether a parameter value equals a particular string
IfParamEqual() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
IfParamEquals - Class in org.anchoranalysis.plugin.image.bean.channel.provider
 
IfParamEquals() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
 
IfPredicateBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
Base class which multiplexes between the current mask and an alternative depending if a condition is met.
IfPredicateBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
 
ifPresent(Optional<S>, CheckedConsumer<S, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Like Optional.map(java.util.function.Function<? super T, ? extends U>) but tolerates an exception in the mapping function, which is immediately thrown.
ifPresentSingle(String, CheckedConsumer<String, E>) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter
Executes a Consumer if an option is present.
IfStackExists - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
The current mask is a particular stack exists (at least one ON voxel) otherwise maskElse is returned.
IfStackExists() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
 
IfVoxelZero - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Creates a new channel which is a merged version of two input channels according to rules.
IfVoxelZero() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
 
ignoreAtThreshold - Variable in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3Base
Disconsiders anything outside the threshold.
IgnoreUnderscorePrefix - Class in org.anchoranalysis.io.output.bean.enabled
All outputs are allowed unless the name's first character is an underscore.
ImageAssignLabel<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
Assigns a label to each image and optionally 1.
ImageAssignLabel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
 
ImageBean<T> - Class in org.anchoranalysis.image.bean
 
ImageBean() - Constructor for class org.anchoranalysis.image.bean.ImageBean
 
ImageCSVLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
 
ImageCSVLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
 
ImageCSVLabellerInitParams - Class in org.anchoranalysis.plugin.image.task.labeller
 
ImageCSVLabellerInitParams(FileLabelMap<String>) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
 
ImageFileShape - Class in org.anchoranalysis.io.bioformats.copyconvert
How to shape the image (across various dimensions) after the copying
ImageFileShape(Dimensions, int, int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
 
ImageInitParams - Class in org.anchoranalysis.image.bean.nonbean.init
 
ImageInitParams(SharedObjects) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
ImageIOWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer
 
ImageIOWriter() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter
 
ImageJRasterWriter - Class in org.anchoranalysis.io.imagej.bean.stack.writer
Base class for writing a raster using ImageJ.
ImageJRasterWriter() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
 
ImageLabelAnnotation - Class in org.anchoranalysis.annotation.image
A single label that pertains to an image.
ImageLabelAnnotation(String) - Constructor for class org.anchoranalysis.annotation.image.ImageLabelAnnotation
 
ImageLabeller<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
Associates a label with an image.
ImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
 
ImageLabellerStringMap<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
Maps one set of labels to another
ImageLabellerStringMap() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
 
ImageLabellerStringMapInitParams<T> - Class in org.anchoranalysis.plugin.image.task.labeller
 
ImageLabellerStringMapInitParams(Map<String, String>, T) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
 
ImageMoments - Class in org.anchoranalysis.math.moment
The first moment (mean) and eigenvalues of the second moments (covariance) from a matrix of points
ImageMoments(DoubleMatrix2D, boolean, boolean) - Constructor for class org.anchoranalysis.math.moment.ImageMoments
Calculates the second-moments from the covariance of a matrix of points
ImageMomentsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
A base class for features that are calculated using image-moments
ImageMomentsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
 
ImageSize - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
Summarizes the size of images.
ImageSize() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
 
ImgLib2Lanczos - Class in org.anchoranalysis.image.bean.interpolator
 
ImgLib2Lanczos() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
 
ImgLib2Linear - Class in org.anchoranalysis.image.bean.interpolator
 
ImgLib2Linear() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
 
immutableAdd(Point2i, Point2i) - Static method in class org.anchoranalysis.spatial.point.Point2i
Performs an addition without changing any values in an existing point
immutableAdd(Point3d, int, int, int) - Static method in class org.anchoranalysis.spatial.point.Point3d
Performs an addition without changing any values in an existing point
immutableAdd(ReadableTuple3i, int, int, int) - Static method in class org.anchoranalysis.spatial.point.Point3i
Performs an addition without changing any values in an existing point
immutableAdd(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.Point3i
Performs an addition without changing any values in an existing point
immutableAdd(Tuple3d, Tuple3d) - Static method in class org.anchoranalysis.spatial.point.Point3d
Performs an addition without changing any values in an existing point
immutableScale(ReadableTuple3i, int) - Static method in class org.anchoranalysis.spatial.point.Point3i
Performs a scale without changing any values in an existing point
immutableScale(Tuple3d, int) - Static method in class org.anchoranalysis.spatial.point.Point3d
Performs a scale without changing any values in an existing point
immutableSubtract(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.Point3i
Performs a subtraction without changing any values in an existing point
immutableSubtract(Tuple3d, Tuple3d) - Static method in class org.anchoranalysis.spatial.point.Point3d
Performs a subtraction without changing any values in an existing point
imposeMinima(Channel, SeedCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition
 
imposeMinima(Channel, SeedCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
 
ImposeMinima - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
Imposes minima in seed locations on the input-channel before performing the segmentation
ImposeMinima() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
 
imposeMinimumRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
ImposeResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
 
ImposeResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
IncludeBeanFactory - Class in org.anchoranalysis.bean.xml.factory
 
IncludeBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.IncludeBeanFactory
 
includeFirst() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
 
includeFirstOrSecond() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
 
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
Iff true, group columns are added to the CSV exports, and other group exports may occur in sub-directories.
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
 
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
 
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
If either a group-generator is defined or there's more than one provider, then groups should be included
IncludeListFactory<T> - Class in org.anchoranalysis.bean.xml.factory
 
IncludeListFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.IncludeListFactory
 
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
 
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
 
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
 
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
 
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
 
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
 
IncludeMarksFailureException - Exception in org.anchoranalysis.mpp.feature.addcriteria
 
IncludeMarksFailureException(Exception) - Constructor for exception org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException
 
IncludeMarksFailureException(String) - Constructor for exception org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException
 
includeMerged() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
 
includePossiblyOverlappingObject(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
 
includePossiblyOverlappingObject(T, T) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
 
includePossiblyOverlappingObject(T, T) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
Whether to include another (possibly-overlapping with source) element in processing?
IncludeRandomObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points
1.
IncludeRandomObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
 
includeSecond() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
 
IncompleteElementRange - Interface in org.anchoranalysis.io.manifest.sequencetype
An incomplete range of discrete integers (like BoundedRangeIncomplete but with a string-representation for each index.
IncorrectImageSizeException - Exception in org.anchoranalysis.image.core.dimensions
 
IncorrectImageSizeException(Exception) - Constructor for exception org.anchoranalysis.image.core.dimensions.IncorrectImageSizeException
 
IncorrectImageSizeException(String) - Constructor for exception org.anchoranalysis.image.core.dimensions.IncorrectImageSizeException
 
IncorrectVoxelTypeException - Exception in org.anchoranalysis.image.voxel.datatype
 
IncorrectVoxelTypeException(String) - Constructor for exception org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException
 
IncorrectVoxelTypeException(Throwable) - Constructor for exception org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException
 
incr(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
incr(Reporting<S>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
 
incrCount(T) - Method in class org.anchoranalysis.plugin.io.summarizer.FrequencyMap
 
IncreaseFeatureCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
 
IncreaseFeatureCondition(FeatureEvaluator<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
 
increasingIntegers(OutputPatternIntegerSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
 
IncreasingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
Indices must be integers that always increase as added.
IncreasingIntegers() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
 
increment() - Method in class org.anchoranalysis.math.arithmetic.Counter
 
increment(double) - Method in class org.anchoranalysis.math.arithmetic.RunningSum
Adds a new item to the sum, and increments the count by 1.
increment(double, long) - Method in class org.anchoranalysis.math.arithmetic.RunningSum
Increments both the sum and count by particular values
increment(RunningSum) - Method in class org.anchoranalysis.math.arithmetic.RunningSum
Increments (adds) an existing RunningSum to the current.
increment(Point2d) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
 
increment(Point2i) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
 
increment(Point3d) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
 
increment(Point3i) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
 
increment(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
incrementCount(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
 
incrementingByOne(OutputPatternIntegerSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
Writes elements to directory, with an incrementing integer in the filename.
incrementingByOneCurrentDirectory(String, String, int) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
Writes elements to the current directory, with an incrementing integer in the filename.
incrementingByOneStream(OutputPatternIntegerSuffix, Stream<T>) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
Writes file for each element in a stream with an incrementing integer sequence in the outputted file-name.
incrementingIntegers(OutputPatternIntegerSuffix, int, int) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
 
IncrementingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
 
IncrementingIntegers() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
IncrementingIntegers(int) - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
IncrementingIntegers(int, int) - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
incrementSumBuffer(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
Increments a particular offset in the sum bufffer by a certain amount
incrementValue(int) - Method in class org.anchoranalysis.math.histogram.Histogram
 
incrementValueBy(int, int) - Method in class org.anchoranalysis.math.histogram.Histogram
 
incrementValueBy(int, long) - Method in class org.anchoranalysis.math.histogram.Histogram
long version of incrValBy
incrementX() - Method in class org.anchoranalysis.spatial.point.Point2i
 
incrementX() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
incrementX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
incrementX(int) - Method in class org.anchoranalysis.spatial.point.Point2i
 
incrementX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
incrementY() - Method in class org.anchoranalysis.spatial.point.Point2i
 
incrementY() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
incrementY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
incrementY(int) - Method in class org.anchoranalysis.spatial.point.Point2i
 
incrementY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
incrementZ() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
incrementZ(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
incrementZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
incrEnergy(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
incrKernelAccpt(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
incrKernelProp(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
incrSize(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
incrTemperature(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
incrWorker() - Method in class org.anchoranalysis.core.progress.ProgressReporterMultiple
 
IndependentChannels - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
Converts each channel independently and creates a single-channeled stack from the conversion.
IndependentChannels() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
 
index(int) - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange
Maps an original integer to it's index from (0..size]
Indexable - Class in org.anchoranalysis.core.index
Holds a single-index which is hashable and comparable.
Indexable(int) - Constructor for class org.anchoranalysis.core.index.Indexable
 
IndexableMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy
 
IndexableMarksWithEnergy(int, MarksWithEnergyBreakdown) - Constructor for class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
 
IndexableOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
An output-name with an index somehow appended or prepended in a particular style.
IndexableOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
 
IndexableOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
 
IndexableOutputNameStyle(IndexableOutputNameStyle) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
Copy constructor
IndexableOverlays - Class in org.anchoranalysis.overlay
 
IndexableOverlays(int, OverlayCollection) - Constructor for class org.anchoranalysis.overlay.IndexableOverlays
 
IndexBridge<T> - Class in org.anchoranalysis.core.index
 
IndexBridge(GetterFromIndex<T>) - Constructor for class org.anchoranalysis.core.index.IndexBridge
 
IndexByChannel<T> - Class in org.anchoranalysis.mpp.voxel.partition
 
IndexByChannel() - Constructor for class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
 
IndexByRegion<T> - Class in org.anchoranalysis.mpp.voxel.partition
 
IndexByRegion(VoxelPartitionFactory<T>, int, int) - Constructor for class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
 
IndexedCSVRows - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
Stores the rows from the CSV file.
IndexedCSVRows(ReadByLine, ColumnDefinition) - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.csv.IndexedCSVRows
Creates an index of the rows of the CSV file according to a particular columnDefinition
IndexedRegionBase - Class in org.anchoranalysis.plugin.mpp.bean.region
MarkRegion with a region and an index
IndexedRegionBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
IndexGettableSettable - Interface in org.anchoranalysis.core.index
 
IndexGetter - Interface in org.anchoranalysis.core.index
 
indexIncr(String) - Method in class org.anchoranalysis.io.generator.sequence.SequenceMemory
 
indexInitialPoint() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
 
indexOf(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
indexOf(String) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex
The index for a particular featureName
indexOf(Mark) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
indexOf(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
IndexSetter - Interface in org.anchoranalysis.core.index
 
IndirectlyFromListBeanFactory<T extends AnchorBean<T>,​S> - Class in org.anchoranalysis.bean.xml.factory
 
IndirectlyFromListBeanFactory(CheckedFunction<List<T>, S, ? extends Exception>) - Constructor for class org.anchoranalysis.bean.xml.factory.IndirectlyFromListBeanFactory
 
informLatestState(T) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
Called every time a proposal is accepted, so a kernel can potentially keep track of the state of the current image
informLatestState(T) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelIndependent
 
init() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
init() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
init() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationCondition
 
init() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
 
init() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
 
init(Path) - Method in class org.anchoranalysis.io.manifest.Manifest
 
init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
 
init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
 
init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
Should be called once before calling any other methods
init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
 
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.image.feature.bean.score.VoxelScore
Initializes the voxels-score.
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
 
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
 
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
 
init(List<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
 
init(List<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
 
init(List<WithConfidence<BoundingBox>>) - Method in class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
 
init(List<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
Called before the operation begins with all proposals
init(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
 
init(Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition
 
init(Logger) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
 
init(FeatureInitParams, Logger) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
Initialises the cache.
init(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
 
init(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
 
init(FeatureInitParams, Feature<T>, Logger) - Method in interface org.anchoranalysis.feature.calculate.InitializableFeature
 
init(ArrangeStack, List<RGBStack>) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.RasterArranger
 
init(Mask) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
init(Mask) - Method in class org.anchoranalysis.mpp.bean.points.updatable.UpdatablePointsContainer
 
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
 
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
 
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
 
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
 
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
 
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
 
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3ZOnly
 
init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
 
init(Generator<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
 
init(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
 
init(MPPInitParams, Logger) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ListBoundCalculator
 
init(VoxelPartitionFactory<T>, int, int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
 
init(KernelBirth<T>, KernelDeath<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
Must be called before makeProposal
init(P, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean
 
init(T, Logger) - Method in interface org.anchoranalysis.bean.initializable.params.ParamsInitializer
 
initBeanInstance(Object, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
 
initBeforeCalc(KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
 
initBeforeCalc(KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelIndependent
 
initBeforeCalc(KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
InitException - Exception in org.anchoranalysis.core.exception
An exception that occurs when initializing something, and it doesn't succeed
InitException(String) - Constructor for exception org.anchoranalysis.core.exception.InitException
 
InitException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.InitException
 
InitException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.InitException
 
initHeaders(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
 
initHeaders(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
 
initHeaders(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
 
InitializableBean<B,​P extends BeanInitParams> - Class in org.anchoranalysis.bean.initializable
A bean that must be initialized with some parameters before being used.
InitializableBean(PropertyInitializer<P>, PropertyDefiner) - Constructor for class org.anchoranalysis.bean.initializable.InitializableBean
 
InitializableFeature<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate
A feature that should be initialized with FeatureInitParams (or a sub-class) before any calculations occur.
initializePhase(int) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
Initialize the next phase of the algorithm by clearing the committed workers and jobs sets and by initializing the slack arrays to the values corresponding to the specified root worker.
initializerForMPPBeans() - Static method in class org.anchoranalysis.mpp.bean.MPPBean
Creates a property-initializes for MPP-Beans
initialKernel() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
InitParamsHelper - Class in org.anchoranalysis.image.feature.session
 
InitParamsWithEnergyStack - Class in org.anchoranalysis.plugin.image.task.feature
 
InitParamsWithEnergyStack(EnergyStack, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
 
InitParamsWithEnergyStack(ImageInitParams, EnergyStack) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
 
initRecursive(Logger) - Method in class org.anchoranalysis.bean.NullParamsBean
 
initRecursive(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
initRecursive(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.shared.SharedFeatureSet
 
initRecursive(P, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean
Inits this object, and all children objects, so long as they have P Once a Bean doesn't have P, the children are not evaluated
initRecursiveWithInitializer(PropertyInitializer<?>, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean
Initializes the bean and recursively all contained beans (who have compatible initialization requirements)
initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked
The value and offset for the source point (around which we process neighbors)
initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute
The value and offset for the source point (around which we process neighbors)
initSource(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
initSource(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
 
initSource(Point3i, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor
Specify the source-point (of which all the processed points are neighbors)
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
 
initWithProposerSharedObjects(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
INPUT_IMAGE - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
 
INPUT_IMAGE_MASK - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
 
INPUT_IMAGE_VISUAL - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
 
InputBound<T,​S> - Class in org.anchoranalysis.experiment.task
Input for executing a task, associated with shared-state and other parameters.
InputBound(T, S, Manifest, boolean, InputOutputContextStateful) - Constructor for class org.anchoranalysis.experiment.task.InputBound
 
InputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.io
SelectParam<Path> factory for inputs.
InputForMPPBean - Interface in org.anchoranalysis.mpp.io.input
The input can be used to initialize an MPP Bean
inputName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
 
InputOutputContext - Interface in org.anchoranalysis.io.output.outputter
A context for performing input generally and outputting to a particular output-directory.
InputOutputContextStateful - Class in org.anchoranalysis.experiment.task
This exists as an implementation of InputOutputContext that exposes a StatefulMessageLogger.
InputOutputContextStateful(ExperimentExecutionArguments, Outputter, StatefulMessageLogger, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.task.InputOutputContextStateful
 
InputOutputContextSubdirectoryCache - Class in org.anchoranalysis.io.output.outputter
Caches a InputOutputContext for each subdirectory as they are created.
InputOutputContextSubdirectoryCache(InputOutputContext, ManifestDirectoryDescription, boolean) - Constructor for class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache
 
InputOutputExperiment<T extends InputFromManager,​S> - Class in org.anchoranalysis.experiment.bean.io
An experiment that uses both an InputManager to specify inputs and a OutputManager to specify outputting.
InputOutputExperiment() - Constructor for class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
 
InputProcessContext<S> - Class in org.anchoranalysis.plugin.image.task.feature
 
InputProcessContext(ExportFeatureResultsAdder, S, FeatureNameList, Optional<String>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
 
inputs(ImageInitParams, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
 
inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
 
inputSelectParam(CommandLine, String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
Can point to either: a path ending in .xml, assumed to BeanXML for an input manager a directory, set as an the inputDirectory in the input-context a string with a wild-card, assumed to be a glob, set into the input-context as a glob a string with a period and without any forward or backwards slashes, set into the input-context as an extension to match
inputType() - Method in class org.anchoranalysis.feature.bean.Feature
The class corresponding to feature input-type (i.e.
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
 
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
 
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureOperator
 
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
 
inputType() - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
 
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureEnergy
 
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureHistogram
 
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
 
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
 
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
 
inputType() - Method in class org.anchoranalysis.image.feature.bean.stack.FeatureStack
 
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
 
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
 
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
 
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
 
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
 
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureMark
 
inputType() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
 
inputType() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
 
inputType() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
 
inputTypesExpected() - Method in class org.anchoranalysis.experiment.bean.task.HelloWorld
 
inputTypesExpected() - Method in class org.anchoranalysis.experiment.bean.task.Task
Highest class(es) that will function as a valid input.
inputTypesExpected() - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
Highest class(es) that will function as a valid input.
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
 
inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
 
InputTypesExpected - Class in org.anchoranalysis.experiment.task
A list of base (parent) classes for input-types that a task expects
InputTypesExpected(Class<? extends InputFromManager>) - Constructor for class org.anchoranalysis.experiment.task.InputTypesExpected
 
insertAfter(List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
Inserts points at end of existing path.
insertBefore(List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
Inserts points before existing path.
insertBeginning(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList
Inserts a new feature-name at the beginning of the list
insertBeginning(String[]) - Method in class org.anchoranalysis.feature.name.FeatureNameList
Inserts new feature-names at the beginning of the list
InsertRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive
Generates an out string where $digit$ is replaced with the #digit group from a regex
InsertRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
 
InsertRegExGroups(RegEx, String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
 
InsideBoxOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
Creates a binary img-channel where all pixels are 'on' within a certain x, y, z coordinate range
InsideBoxOn() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
 
inSlices - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
 
instance - Static variable in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
 
instance() - Static method in class org.anchoranalysis.bean.initializable.params.NullInitParams
 
instance() - Static method in class org.anchoranalysis.feature.input.FeatureInputNull
 
instance() - Static method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
 
instance() - Static method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
Singleton
instance() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
Singleton
instance() - Static method in class org.anchoranalysis.io.bioformats.ConfigureBioformatsLogging
 
instance() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMapSingleton
 
instance() - Static method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
 
instance() - Static method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
 
INSTANCE - Static variable in class org.anchoranalysis.experiment.task.NoSharedState
 
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
 
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType
 
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType
 
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType
 
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType
 
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.All
A singleton instance of All.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix
A singleton instance of IgnoreUnderscorePrefix.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.None
A singleton instance of None.
INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.rules.Permissive
A singleton instance of Permissive.
InsufficientPointsException - Exception in org.anchoranalysis.mpp.bean.points.fitter
 
InsufficientPointsException() - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
 
InsufficientPointsException(String) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
 
InsufficientPointsException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
 
InsufficientPointsException(Throwable) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
 
IntBinaryOperation - Interface in org.anchoranalysis.core.functional.checked
A binary operation on two int-values that produces an int
IntegerRange - Class in org.anchoranalysis.plugin.io.multifile
 
IntegerRange(int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
 
IntegerRange(int, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
 
IntegerSequenceContaner - Class in org.anchoranalysis.core.index.bounded
 
IntegerSequenceContaner(int) - Constructor for class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
 
integerSet() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
IntegerSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
Outputs a file-name involving an integer of length numberDigits with leading zeros.
IntegerSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
 
IntegerSuffixOutputNameStyle(String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
 
IntegerSuffixOutputNameStyle(String, String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
 
Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
Calculates a statistic from the intensity values covered by a single object-mask in a channel.
Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
The intensity of a particular channel of the stack, by default the mean-intensity.
Intensity - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
Intensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
 
Intensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
 
Intensity() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
 
IntensityGradientBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
 
IntensityGradientBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
IntensityGreaterEqualThan - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
Only keep objects where at least one voxel (on a particular channel) has intensity greater or equal to a threshold.
IntensityGreaterEqualThan() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
 
intensityMax(Voxels<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Finds the maximum intensity-value (as an int) among all voxels.
IntensityMeanCalculator - Class in org.anchoranalysis.plugin.image.intensity
 
IntensityMeanMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
 
IntensityMeanMaxSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
 
IntensityMeanShell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMeanShell() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShell
 
IntensityMeanShellBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
Constructs a shell around an object-mask using a standard dilation and erosion process
IntensityMeanShellBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
 
IntensityMeanShellMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMeanShellMaxSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
 
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in interface org.anchoranalysis.image.voxel.interpolator.Interpolator
Interpolates from voxelsSource to voxelsDestination for unsigned 8-bit buffers.
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
 
interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
 
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in interface org.anchoranalysis.image.voxel.interpolator.Interpolator
Interpolates from voxelsSource to voxelsDestination for unsigned 16-bit buffers.
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
 
interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
 
InterpolateUtilities - Class in org.anchoranalysis.image.voxel.interpolator
 
Interpolator - Interface in org.anchoranalysis.image.voxel.interpolator
 
InterpolatorBean - Class in org.anchoranalysis.image.bean.interpolator
 
InterpolatorBean() - Constructor for class org.anchoranalysis.image.bean.interpolator.InterpolatorBean
 
InterpolatorBeanImageJ - Class in org.anchoranalysis.plugin.imagej.bean.interpolator
 
InterpolatorBeanImageJ() - Constructor for class org.anchoranalysis.plugin.imagej.bean.interpolator.InterpolatorBeanImageJ
 
InterpolatorFactory - Class in org.anchoranalysis.image.voxel.interpolator
 
InterpolatorImgLib2 - Class in org.anchoranalysis.image.voxel.interpolator
Performs interpolation using ImgLib2
InterpolatorImgLib2(InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>, InterpolatorFactory<UnsignedShortType, RandomAccessible<UnsignedShortType>>) - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
 
InterpolatorImgLib2Lanczos - Class in org.anchoranalysis.image.voxel.interpolator
 
InterpolatorImgLib2Lanczos() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Lanczos
 
InterpolatorImgLib2Linear - Class in org.anchoranalysis.image.voxel.interpolator
 
InterpolatorImgLib2Linear() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Linear
 
InterpolatorImgLib2NearestNeighbor - Class in org.anchoranalysis.image.voxel.interpolator
 
InterpolatorImgLib2NearestNeighbor() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2NearestNeighbor
 
InterpolatorNone - Class in org.anchoranalysis.image.voxel.interpolator
Doesn't do any interpolation, just copies values
InterpolatorNone() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
 
intersect(ObjectMask, Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Intersects this object-mask with another
IntersectingCircleObjectsFixture - Class in org.anchoranalysis.test.feature.plugins.objects
 
intersection() - Method in class org.anchoranalysis.spatial.box.BoundingBox
For evaluating the intersection between this bounding-box and others
Intersection - Class in org.anchoranalysis.plugin.image.bean.object.match
 
Intersection - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair
Finds the intersection of two objects and calculates a feature on it
Intersection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Intersection
 
Intersection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
 
IntersectionOverUnion - Class in org.anchoranalysis.plugin.image.box
Calculates the intersection-over-union score a pair of bounding-boxes.
intersectsWith(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
All objects that intersect with another object.
intersectsWith(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
 
intersectsWith(BoundingBox) - Method in class org.anchoranalysis.spatial.rtree.RTree
 
IntersectsWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
Keeps objects which intersects with ANY ONE of a collection of other objects.
IntersectsWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
 
intersectsWithAsIndices(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
 
IntersectsWithContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
Returns only the objects that intersect with at least one object in the container
IntersectsWithContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
 
intersectWith(Extent) - Method in class org.anchoranalysis.spatial.Extent
Intersects this extent with another (i.e.
intFromDoubleCeil(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
intFromDoubleFloor(Point2d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
intFromDoubleFloor(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
intFromFloat(Point3f, boolean) - Static method in class org.anchoranalysis.spatial.point.PointConverter
 
INVALID_AXIS_INDEX - Static variable in class org.anchoranalysis.spatial.axis.AxisTypeConverter
 
INVALID_AXIS_STRING - Static variable in class org.anchoranalysis.spatial.axis.AxisTypeConverter
 
invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
Invalidates existing caches so all calculations occur freshly
invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.ResettableCalculation
Resets the cached-calculation, so the next call to doOperationWithParams() is guaranteed to calculation the operation, and store the value in the cache.
invalidate() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
 
invalidate() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
Invalidates the cache, removing any items already stored.
invalidate() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
 
invalidate() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
 
invalidateExcept(Set<ChildCacheName>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
Invalidates existing caches so all calculations occur freshly - except some particular child-caches who are not invalidated
invalidateExcept(Set<ChildCacheName>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
 
invalidateExcept(Set<ChildCacheName>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
 
InvalidPathArgumentException - Exception in org.anchoranalysis.launcher.executor.selectparam.path
An exception throw if an invalid-path is inputted as an argument.
InvalidPathArgumentException(String, InvalidPathException) - Constructor for exception org.anchoranalysis.launcher.executor.selectparam.path.InvalidPathArgumentException
 
invert() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
Changes the OFF state to be the ON state and vice-versa.
invert() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
 
invert() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Produces a new object-mask that uses the same voxel-buffer but inverts the OFF and ON
invert() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
 
invert(Mask) - Static method in class org.anchoranalysis.image.core.mask.MaskInverter
Modifies a mask so that OFF voxels become ON voxels and vice versa
Invert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
Subtracts each voxel from the maximum value for the channel's data type (e.g.
Invert - Class in org.anchoranalysis.plugin.image.bean.mask.provider
Switches on voxels to off and vice-versa.
Invert - Class in org.anchoranalysis.plugin.image.bean.segment.binary
Performs a segmentation and inverts and ON and OFF bytes
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
 
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
 
Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
 
InvertedMax<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
InvertedMax() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
 
invertObjectDuplicate(ObjectMask) - Static method in class org.anchoranalysis.image.core.mask.MaskInverter
Creates a new object-mask where OFF voxels become ON voxels and vice versa
isAccepted() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
 
isAccepted() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
 
isAccepted() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
isAcceptNoResolution() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
 
isAcceptOutsideScene() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
 
isAddName() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
isAddOne() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
 
isApplyResolution() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
Multiples the values by the x-resolution, if it exists.
isAsPercentage() - Method in class org.anchoranalysis.feature.bean.results.Quantile
If true, the quantile is interpreted as a percentage rather than a decimal
isAtLeastOnePositive() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
Checks that at least one of iterationsDilation and iterationsErosion is more than 0
isAvoidBulletOnFirst() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
Iff true no bullet is added for the very first-item in the list
isAvoidDivideByZero() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
 
isAvoidOverlappingObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
If true, no overlapping objects are treated as pairs
isBest() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
isBest() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
isBigNeighborhood() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
iff true uses a big-neighborhood (8 or 26 connectivity) for dilation
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
 
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
If true uses 8 neighborhood rather than 4 neighborhood etc.
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
if true, uses 8 neighborhood instead of 4, and similarly in 3d
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
 
isBigNeighborhood() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
isBit0() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
isBit1() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
isBit2() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
isBit3() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
isBit4() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
isBit5() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
isBit6() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
isBit7() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
 
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
 
isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ
 
isBySlices() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
 
isCalledRegisterAllPackage() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
 
isCellUsed(int, int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
 
isChangeExisting() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
If true, the existing channel can be changed.
isClearOutsideMask() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
 
isClosed() - Method in class org.anchoranalysis.spatial.Contour
 
isCollapseFilename() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
isCompatibleWith(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
Can these parameters be used with a particular feature?
isCompatibleWith(Mark) - Method in interface org.anchoranalysis.mpp.mark.CompatibleWithMark
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.EllipseBoundsCheck
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceAbstractPosition
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceRadii
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.CreateNew
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.UniformRandom
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomXY
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelReplacePartition
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ConstantWeight
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.NumberPoints
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
isCompleted() - Method in class org.anchoranalysis.experiment.task.processor.JobState
 
isCompletedFailure() - Method in class org.anchoranalysis.experiment.task.processor.JobState
 
isCompletedSuccessfully() - Method in class org.anchoranalysis.experiment.task.processor.JobState
 
isConditionTrue() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
 
isConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
 
isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
isConsiderForMerge() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
 
isConvexHull() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
If true, Reduces the set of points by applying a convex-hull operation
isCov() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
 
isCreateShort() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
 
isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
 
isCreateShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
If True creates an unsigned short-image
isCsvIgnoreZeros() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
Iff true, bins with zero-counts are not written as a row in the CSV file.
isDatasetNameSubdirectory() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
If true the datasetName is appended as a subdirectory e.g.
isDay() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
If true, the current day (yyyy.MM.dd) is included in the output
isDebug() - Method in class org.anchoranalysis.bean.shared.path.RootPath
If true this root is preferred, when executing a job in debugging mode
isDebug() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
isDebugEnabled() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
 
isDebugEnabled() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
Is debug-mode enabled?
isDebugEnabled() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
isDebugMode() - Method in class org.anchoranalysis.io.output.path.prefixer.FilePathPrefixerContext
 
isDebugModeEnabled() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
isDefault() - Method in class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
 
isDefault() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam
Is this the default option that occurs without any additional user effort?
isDefault() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
 
isDetailedLogging() - Method in class org.anchoranalysis.experiment.task.InputBound
 
isDetailedLogging() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
Iff true, additional log messages are written to describe each job in terms of its unique name, output folder, average execution time etc.
isDifferentColorsForMatches() - Method in class org.anchoranalysis.annotation.io.assignment.generator.ColorPool
 
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Is this buffer direct or non-direct?
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
Is this buffer direct or non-direct?
isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
 
isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
 
isDisablePathModification() - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
 
isDo3D() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
isDo3D() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
 
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
Whether to perform the morphological dimensions in 3D or 2D
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
 
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
 
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
 
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
 
isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
 
isDo3D() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
 
isDummyMode() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
isEmpty() - Method in interface org.anchoranalysis.bean.StringBeanCollection
 
isEmpty() - Method in class org.anchoranalysis.bean.StringList
 
isEmpty() - Method in class org.anchoranalysis.bean.StringSet
 
isEmpty() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
Are there any items in the provider
isEmpty() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
isEmpty() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
 
isEmpty() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
isEmpty() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
 
isEmpty() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
isEmpty() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
If no output-names exist.
isEmpty() - Method in class org.anchoranalysis.math.histogram.Histogram
 
isEmpty() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
isEmpty() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
isEmpty() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
 
isEmpty() - Method in class org.anchoranalysis.spatial.box.PointRange
Has a valid min and max defined? In other words, has at least one point been added?
isEmpty() - Method in class org.anchoranalysis.spatial.Extent
 
isEnabled() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
 
isErodeAtBoundary() - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
 
isErrorDisconnectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
If true, throws an error if there is a disconnected object after the erosion
isEvaluated() - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
 
isExceptionIfEmpty() - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
If true, then an exception is thrown if the histogram is empty, otherwise is returned.
isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
Iff true, zero-valued voxels are excluded from the histogram
isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
 
isExcludeZero() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
If true, zeros are excluded from considering in the histogram
isExecuting() - Method in class org.anchoranalysis.experiment.task.processor.JobState
 
isExitBeforeOptimization() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Iff true the algorithm exits before optimization begins (useful for debugging).
isExitWithMinima() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
If true, exits early and just returns the minima, without any further segmentation
isExtendInZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all slices)
isFindMaxima() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
If true, the maxima of the score is searched for.
isFinished() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
 
isFirst() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
Iff true, first object is used, otherwise the second
isFirstLineHeaders() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
isFixRandomSeed() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Iff true uses a constant seed for the random-number-generator (useful for debugging).
isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced
isForceBinary() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
isForceChangeBytes() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
isForceDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
Whether more detailed log-messages around each experiment occur.
isForceEagerEvaluation() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
isForceRGB() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
If set, ensures every stack is converted into 3 channels
isForwardDirectionOnly() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
isGaussian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
If true, the Gaussian filter is included
isGPU() - Method in class org.anchoranalysis.core.concurrency.WithPriority
 
isHighestTwoRadiiOnly() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
 
isIgnoreAtThreshold() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
 
isIgnoreAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
 
isIgnoreCase() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
 
isIgnoreFileNotFoundAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
isIgnoreFittingFailure() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply not included (with only a log error) If false, an exception is thrown
isIgnoreHidden() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
 
isIgnoreHigherSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
 
isIgnoreLowerSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
 
isIgnoreMissingChannel() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
Iff true and we cannot find a channel in the file, we ignore it and carry on
isIgnoreNaN() - Method in class org.anchoranalysis.feature.bean.operator.Sum
If true, we ignore any NaN values.
isIgnoreNoObjects() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
If true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
isIgnoreRangeAxisOutside() - Method in class org.anchoranalysis.plot.index.LinePlot
 
isIgnoreZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
 
isIncludeFeatureNames() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features
isIncludeFileName() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
 
isIncludeFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Include features for the First-object of the pair
isIncludeFolders() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
If false, the folders are ignored, and only the file-name is used in the output
isIncludeMerged() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Include features for the Merged-object of the pair
isIncludeSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Include features for the Second-object of the pair
isIncludeShell() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
isIncludeZ() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
 
isInitialized() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
 
isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
Is an input-object compatible with this particular task?
isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.bean.task.Task
Is an input-object compatible with this particular task?
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
 
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
 
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
 
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
 
isInterpolate() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
 
isInverse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
 
isInverse() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is removed)
isInverseMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
 
isInvert() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
 
isInvert() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
 
isInvert() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
Iff true, then a file is rejected if regEx matches and vice-versa (opposite to normal behaviour)
isInvertDecisionValue() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
 
isItemIncluded(T) - Method in class org.anchoranalysis.plot.bean.Plot
Whether to include this particular item in the plot?
isKeepEntireImage() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
If true, rather than writing out a bounding-box around the object-mask, the entire image is written
isKeepExtremes() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
isKeepZ() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
Keep the z-resolution if it is already defined
isKeyRequired() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
isLabel() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
If true a label is added beside every image showing the slice index
isLeaf() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
isLogPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
if true, the pathIn and pathOut are logged.
isMarksSpan() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
isMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
isMedian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
If true, the median filter is included
isMemberFlag(byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
 
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
 
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr
 
isMemberFlagAnd(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
 
isMemberFlagOr(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
 
isMerge() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
 
isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
 
isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
isMip() - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
 
isMip() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
 
isMip() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
 
isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
 
isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
 
isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodIgnoreOutsideScene
 
isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
 
isNewValuesPossible() - Method in interface org.anchoranalysis.image.voxel.interpolator.Interpolator
Returns true if it's possible for values to be created after interpolation that aren't found in the input-image.
isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Lanczos
 
isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Linear
 
isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2NearestNeighbor
 
isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
 
isNoBlack() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
 
isNormalize() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
isNormalize() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
 
isNormalizeFeatures() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
Normalize features
isNoScale() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
If the scale-factor involves no scaling at all
isNumeric() - Method in class org.anchoranalysis.core.value.TypedValue
 
isNumeric() - Method in class org.anchoranalysis.io.output.bean.ReportFeature
 
isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
 
isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
 
isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
 
isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
 
isNumeric() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
 
isNumeric() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
 
isNumeric() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
 
isOff(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
 
isOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
 
isOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
 
isOn() - Method in interface org.anchoranalysis.io.generator.sequence.OutputSequence
 
isOn() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
 
isOn() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
 
isOn(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
 
isOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
 
isOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
 
isOutline() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
If true, an outline is drawn around the entries.
isOutlineAtBoundary() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
 
isOutputCSV() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
Iff true, a mapping.csv file is created showing the mapping between the original-names and the anonymized versions
isOutputEnabled() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.All
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.None
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet
 
isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelNot
 
isOutputEnabled(String) - Method in interface org.anchoranalysis.io.output.enabled.single.SingleLevelOutputEnabled
Is a particular a particular output-enabled?
isOutputShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
Iff true, outputs a short channel, otherwise byte channel
isOutsideAtThreshold() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
 
isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
 
isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
 
isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
 
isParamPrefixAppendNumber() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
If true the constant is appended to the param prefix (a dot and a number)
isPhysical() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
 
isPlateau(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
 
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
 
isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
Is the payload considered in making decisions? (iff false, payload of nodes is irrelvant)
isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
 
isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>, boolean) - Static method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
 
isPointInside(DrawOverlay, Point3i) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
 
isPointInside(DrawOverlay, Point3i) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
 
isPointInside(DrawOverlay, Point3i) - Method in class org.anchoranalysis.overlay.Overlay
Is a point inside an overlay? (for a particular OverlayWriter).
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.Mark
 
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
isPointOn(Point3i) - Method in class org.anchoranalysis.image.core.mask.Mask
 
isPointOnMask(Point3d, EnergyStack, Function<Point3d, Point3i>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
 
isPrefix() - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
If true, a prefix is prepended to the name of each added bean.
isPreserveExtensionIfDuplicate() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
Keeps the extension if the file-name (without the extension) becomes duplicated with another
isPreventObjectIntersection() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
Iff true, objects can only be neighbors if they have no intersecting voxels.
isProposal() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
 
isProposed() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
 
isRadiusInMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
 
isRecordedAsEnabled(String) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
Is a particular output-name recorded as enabled?
isRecurseSubfolders() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
 
isRecursive() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
Whether to apply the search recursively or not
isRejectIterationIfAllLow() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
 
isRejectIterationIfDisconnected() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
 
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.EqualTo
 
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.GreaterThan
 
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.GreaterThanEqualTo
 
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.LessThan
 
isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.LessThanEqualTo
 
isRelationToValueTrue(double, double) - Method in interface org.anchoranalysis.math.relation.RelationToValue
 
isRemoveExtensionInDescription() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
Whether to remove the file-extension from the filename.
isRemoveTouchingBorderXY() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
isReplaceMatchesWithSolids() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
isReplaceWithMidpoint() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
 
isReportFitterErrors() - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
isRequireAllFilesMatch() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
isRequireBBoxNeighbors() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch
isRequireTouching() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
Requires the object-masks to touch.
isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceInfinity
 
isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceNaN
 
isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
 
isRewardHigherSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
Treat the higher side as if it's the the fill cdf
isRewardLowerSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
 
isRgb() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
If true, the output contains three channels (the input and two duplicates) instead of one
isRGB() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
isRGB() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
 
isRGB() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
 
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
 
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
 
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
 
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
Is it an image with three channels (red, green and blue)?
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
 
isRootInStructure() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
If true the directory structure is ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
isRotateOnlyIn2DPlane() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
isSecond() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
Only relevant if time==true.
isSecondary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
If proposal is true, this toggles between the primary and secondary proposal
isSelective() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
Whether the output should be checked to see if it is allowed or not.
isShowAgg() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
 
isShowBest() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
 
isShowDomainAxis() - Method in class org.anchoranalysis.plot.index.BarPlot
 
isShowVerticalAxisLines() - Method in class org.anchoranalysis.plot.PlotInstance
 
isSigmaInMeters() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
 
isSilentlyDeleteExisting() - Method in class org.anchoranalysis.io.output.bean.OutputManager
Whether to silently first delete any existing output at the intended path, or rather throw an error.
isSilentlyDeleteExisting() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
isSkipAtBorder() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
If true we do not fill any objects that touch the border
isSkipFileName() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
Iff true the filename is not considered, only the subdirectories.
isSkipFileName() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
isSkipMissingChannels() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
isSlicesSeparately() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
 
isStackAsChannel() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no additionalChannel is set)
isStackBackground() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
isStrongEdgeEnhancer() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
Enables the StrongEdgeEnhancer diffusion function
isSubtractFromMaskOnly() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
 
isSuppress3D() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
isSuppress3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
 
isSuppress3D() - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
 
isSuppressErrors() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
isSuppressExceptions() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
 
isSuppressExceptions() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
 
isSuppressExceptions() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
isSuppressExceptions() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
isSuppressOutlineZ() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
if true, the outline is suppressed in the z-dimension i.e.
isSuppressRes() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
 
isSuppressRootOut() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.
isSuppressSeries() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
If true, the series index is not included in the outputted file-names.
isSuppressSubfolders() - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
 
isSuppressZ() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
 
isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
 
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
 
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
 
isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
If true co-voariance is suprpessed in z-dimension
isSuppressZ() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
 
isSuppressZ() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
 
isSuppressZ() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
 
isSuppressZ() - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
Iff true, surpresses covariance in the z-direction.
isSuppressZCovariance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
isSuppressZCovariance() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
 
isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
 
isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
isTestBothDirections() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
iff true each combination of neighbors is tested only once, otherwise twice
isThrowExceptionForInsufficientPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
 
isThumbnailsEnabled() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
 
isTime() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
If true, the current time (HH.mm.ss) is included in the output
isTransposed() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
isUnbounded() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
 
isUnboundedAtBothEnds() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
 
isUnboundedOrOutsideRange(double) - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
 
isUnboundedOrOutsideRangeAtBothEnds(double) - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
 
isUniformlySized() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
isUniformTyped() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
 
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
 
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
 
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
 
isUnstarted() - Method in class org.anchoranalysis.experiment.task.processor.JobState
 
isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
 
isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
 
isUseMax() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
 
isUseMax() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
 
isUseMIP() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
isUseMIP() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
isUseZ() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
 
isUseZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
 
isUseZ() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
isVaryColors() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
If true the colors change for different objects in the image (using a default color set).
isZOnly() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
 
iterateBins(Histogram.BinConsumer) - Method in class org.anchoranalysis.math.histogram.Histogram
Calls consumer for every bin-value, increasing from min to max.
iterateBinsUntil(int, Histogram.BinConsumer) - Method in class org.anchoranalysis.math.histogram.Histogram
Calls consumer for every bin-value until a limit, increasing from min to limit (inclusive).
iterateMap(Map<K, V>, CheckedBiConsumer<K, V, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
Iterate through all entries in a Map.
iterateOverSlices(Consumer<VoxelBuffer<T>>) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
Calls sliceConsumer once for each slice with the respective buffer
iterateOverSlicesAndOffsets(ProcessVoxelBufferUnary<T>) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
Calls process for each offset in each slice
iterateOverXY(OffsettedScalarTwoDimensionalConsumer<E>) - Method in class org.anchoranalysis.spatial.Extent
Calls processor once for each x and y-values in the range.
iterateOverXY(PointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.Extent
Calls processor once for each x and y-values in the range.
iterateOverXYOffset(CheckedIntConsumer<E>) - Method in class org.anchoranalysis.spatial.Extent
Calls processor once for each x and y-values but only passing an offset.
iterateOverXYOffset(OffsettedPointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.Extent
Calls processor once for each x and y-values in the range.
iterateOverXYWithShift(Point2i, PointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.Extent
Calls processor once for each x and y-values in the range, with a shift added.
iterateOverZ(CheckedIntConsumer<E>) - Method in class org.anchoranalysis.spatial.Extent
Calls processor once for each z-value in the range
iterateOverZUntil(IntPredicate) - Method in class org.anchoranalysis.spatial.Extent
Calls processor once for each z-value in the range unless indexPredicate returns false.
IterateVoxelsAll - Class in org.anchoranalysis.image.voxel.iterator
Utilities for iterating over all voxels in one or more Voxels.
IterateVoxelsBoundingBox - Class in org.anchoranalysis.image.voxel.iterator
Utilities for iterating over the subset of image voxels within a bounding-box.
IterateVoxelsEqualTo - Class in org.anchoranalysis.image.voxel.iterator
Like IterateVoxelsAll but specifically for equal-to operations on Voxels of type UnsignedByteBuffer.
IterateVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
Like IterateVoxelsBoundingBox but specifically for processing areas of intersection between BoundedVoxels of type UnsignedByteBuffer.
IterateVoxelsMask - Class in org.anchoranalysis.image.core.mask
Utilities for iterating over the subset of voxels corresponding to an on state in a Mask.
IterateVoxelsNeighbors - Class in org.anchoranalysis.image.voxel.iterator.neighbor
Utilities for iterating over the neighboring voxels to a given point.
IterateVoxelsObjectMask - Class in org.anchoranalysis.image.voxel.iterator
Utilities for iterating over the subset of voxels corresponding to an on state in an ObjectMask.
IterateVoxelsObjectMaskOptional - Class in org.anchoranalysis.image.voxel.iterator
Utilities for iterating over the subset of voxels corresponding to an on state in an optional ObjectMask.
IterateVoxelsRemaining - Class in org.anchoranalysis.image.voxel.iterator
Utilities for iterating over remaining voxels in one or more VoxelBuffers.
iterator() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
An iterator for each element in the sequence
iterator() - Method in class org.anchoranalysis.bean.StringList
 
iterator() - Method in class org.anchoranalysis.bean.StringSet
 
iterator() - Method in class org.anchoranalysis.core.color.ColorList
 
iterator() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
iterator() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
iterator() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
iterator() - Method in class org.anchoranalysis.feature.io.name.CombinedName
 
iterator() - Method in class org.anchoranalysis.feature.io.name.SimpleName
 
iterator() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
iterator() - Method in class org.anchoranalysis.feature.name.FeatureNameList
 
iterator() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
 
iterator() - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
 
iterator() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
 
iterator() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
iterator() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
iterator() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
iterator() - Method in class org.anchoranalysis.image.core.stack.Stack
 
iterator() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
iterator() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
 
iterator() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
iterator() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
 
iterator() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
iterator() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
 
iterator() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
iterator() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
iterator() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
iterator() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
 
iterator() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
iterator() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
iterator() - Method in class org.anchoranalysis.overlay.OverlayProperties
 
iterator() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
 
iterator() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
 
iterator() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
 
iterator() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
 
iteratorCoupledManifests() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
 
iteratorCoupledManifestsFor(Manifest) - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
 
iteratorExperimentalManifests() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
 

J

JobDescription - Class in org.anchoranalysis.experiment.task.processor
 
JobDescription(String, int) - Constructor for class org.anchoranalysis.experiment.task.processor.JobDescription
 
jobDirectory() - Static method in class org.anchoranalysis.io.manifest.finder.match.DirectoryMatch
 
JobExecutionException - Exception in org.anchoranalysis.experiment
An exception that occurs when a job is executed.
JobExecutionException(String) - Constructor for exception org.anchoranalysis.experiment.JobExecutionException
 
JobExecutionException(String, Throwable) - Constructor for exception org.anchoranalysis.experiment.JobExecutionException
A string message displayed to the user as well as a stack-trace of the cause
JobExecutionException(Throwable) - Constructor for exception org.anchoranalysis.experiment.JobExecutionException
 
JobProcessor<T extends InputFromManager,​S> - Class in org.anchoranalysis.experiment.bean.processor
Processes a job
JobProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.JobProcessor
 
JobRootDirectory - Class in org.anchoranalysis.io.manifest.directory
The root directory for where outputs for a particular experiment occur.
JobRootDirectory() - Constructor for class org.anchoranalysis.io.manifest.directory.JobRootDirectory
 
JobStartStopLogger - Class in org.anchoranalysis.experiment.task.processor
Logs events when jobs start and stop, with or without errors.
JobStartStopLogger(String, ConcurrentJobMonitor, boolean, int, Optional<MessageLogger>) - Constructor for class org.anchoranalysis.experiment.task.processor.JobStartStopLogger
Creates a job-logger.
JobState - Class in org.anchoranalysis.experiment.task.processor
 
JobState() - Constructor for class org.anchoranalysis.experiment.task.processor.JobState
 
JoinRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive
Generates an outstring of the form
JoinRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
 

K

Kernel - Class in org.anchoranalysis.image.voxel.kernel
 
Kernel<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
Modifies an Object by applying a kernel
Kernel() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
 
Kernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.Kernel
 
kernelAccepted(Kernel<S>, Optional<T>, T, TransformationContext) - Method in interface org.anchoranalysis.plugin.mpp.segment.kernel.updater.KernelUpdater
Informs that a proposal from a particular kernel has been accepted
kernelAccepted(Kernel<S>, Optional<T>, T, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.kernel.updater.KernelUpdaterSimple
 
kernelAssigner() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
 
KernelAssigner<S,​T> - Interface in org.anchoranalysis.mpp.segment.kernel
 
KernelAssignerAddErrorLevel<S,​T> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.assigner
 
KernelAssignerAddErrorLevel(KernelAssigner<S, T>, ErrorNode) - Constructor for class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerAddErrorLevel
 
KernelAssignerCalculateEnergyFromKernel<S,​T> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.assigner
 
KernelAssignerCalculateEnergyFromKernel(KernelStateBridge<S, T>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerCalculateEnergyFromKernel
 
KernelBirth<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
Adds a new mark (a "birth") to create a proposal
KernelBirth() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
 
KernelBirthAndKill - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelBirthAndKill() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
KernelBirthPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
Proposes new marks ONLY if they haven't already been proposed and accepted.
KernelBirthPartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
 
KernelBirthPixelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
As an example, this is like sampling WITH replacement.
KernelBirthPixelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
 
KernelBirthPixelized(MarkProposer) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
 
KernelCalculateEnergyException - Exception in org.anchoranalysis.mpp.segment.kernel
 
KernelCalculateEnergyException(String) - Constructor for exception org.anchoranalysis.mpp.segment.kernel.KernelCalculateEnergyException
 
KernelCalculateEnergyException(String, Exception) - Constructor for exception org.anchoranalysis.mpp.segment.kernel.KernelCalculateEnergyException
 
KernelCalculationContext - Class in org.anchoranalysis.mpp.segment.kernel
 
KernelCalculationContext(MarkFactoryContext, EnergyStack, EnergySchemeWithSharedFeatures, RandomNumberGenerator, ErrorNode) - Constructor for class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
 
KernelDeath<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelDeath() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
 
KernelDeath.MarkAnd<S,​T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelDeathPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
 
KernelDeathPartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelDeathPartition
 
KernelDeathPixelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
 
KernelDeathPixelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelDeathPixelized
 
KernelDependent<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
 
KernelDependent() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.KernelDependent
 
KernelDescision - Class in org.anchoranalysis.mpp.segment.kernel.proposer
A description of the decision made to accept/reject a kernel at a particular time instance (index)
KernelDescision(KernelWithIdentifier<?>, boolean, boolean, int[], long, int, ProposerFailureDescription) - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
 
kernelDescription() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
KernelExchange - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelExchange() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
 
kernelIdentifier() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
 
KernelIndependent<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
A kernel that makes proposals independently of the current state
KernelIndependent() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.KernelIndependent
 
KernelInitialMarksFromPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelInitialMarksFromPartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
KernelInitialMarksProposed - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelInitialMarksProposed() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
 
KernelInitialMarksVoxelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelInitialMarksVoxelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
KernelInitialMarksVoxelized(MarkCollectionProposer) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
KernelIterDescriptionSerializerPeriodicReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
KernelIterDescriptionSerializerPeriodicReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.KernelIterDescriptionSerializerPeriodicReporter
 
KernelMerge - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelMerge() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
KernelPosNeg<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
 
KernelPosNeg() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
 
KernelProposer<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel.proposer
 
KernelProposer() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
KernelProposerOption<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel.proposer
 
KernelProposerOption() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
 
KernelProposerOptionDual<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
 
KernelProposerOptionDual() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
KernelProposerOptionSingle<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
 
KernelProposerOptionSingle() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
 
KernelProposerOptionSingle(Kernel<T>, double) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
 
KernelReplace<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelReplace() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
 
KernelReplacePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
 
KernelReplacePartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelReplacePartition
 
KernelSplit - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
KernelSplit() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
kernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
 
kernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
 
kernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
KernelStateBridge<U,​T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
Transforms a kernel-to-state and vice versa
KernelStateBridge() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridge
 
KernelStateBridgeIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
No transformation occurs as Kernel and State are the same type
KernelStateBridgeIdentity() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeIdentity
 
KernelStateBridgePixelize<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
State derived from the kernel takes the form of ToPixelized<T>
KernelStateBridgePixelize() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
 
KernelStateBridgeTransformer<U,​T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
 
KernelStateBridgeTransformer() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
 
kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridge
 
kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeIdentity
 
kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
 
kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
 
KernelUpdater<S,​T> - Interface in org.anchoranalysis.plugin.mpp.segment.kernel.updater
 
KernelUpdaterSimple<S,​T> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.updater
 
KernelUpdaterSimple(ListUpdatableMarkSetCollection, WeightedKernelList<S>, StateTransformer<Optional<T>, Optional<S>>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.kernel.updater.KernelUpdaterSimple
 
KernelWithIdentifier<T> - Class in org.anchoranalysis.mpp.segment.kernel.proposer
 
KernelWithIdentifier(Kernel<T>, int) - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
 
keys() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
Returns a set of keys associated with the provider.
keys() - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
 
keys() - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
 
keys() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
keys() - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
 
keys() - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
 
keys() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
 
keys() - Method in class org.anchoranalysis.image.core.stack.NamedStacks
 
keys() - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequence
 
keys() - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
 
keys() - Method in class org.anchoranalysis.image.core.stack.wrap.WrapTimeSequenceAsStack
 
keySet() - Method in class org.anchoranalysis.core.value.KeyValueParams
 
keySet() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
 
keysEvaluated() - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
 
KeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.params
A key and associated value
KeyValueCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
 
keyValueParams() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
KeyValueParams - Class in org.anchoranalysis.core.value
Parameters represented by key/value strings
KeyValueParams() - Constructor for class org.anchoranalysis.core.value.KeyValueParams
 
KeyValueParamsDeserializer<T> - Class in org.anchoranalysis.core.serialize
 
KeyValueParamsDeserializer() - Constructor for class org.anchoranalysis.core.serialize.KeyValueParamsDeserializer
 
KeyValueParamsForImageCreator - Class in org.anchoranalysis.mpp.feature.energy.scheme
Creates KeyValueParams for a particular EnergyStack that is associated with a EnergyScheme
KeyValueParamsForImageCreator(EnergyScheme, SharedFeatureMulti, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.KeyValueParamsForImageCreator
 
KeyValueParamsGenerator - Class in org.anchoranalysis.io.generator.serialized
 
KeyValueParamsGenerator(String) - Constructor for class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
 
KeyValueParamsInitParams - Class in org.anchoranalysis.bean.shared.params.keyvalue
 
KeyValueParamsProvider - Class in org.anchoranalysis.bean.shared.params.keyvalue
 
KeyValueParamsProvider() - Constructor for class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProvider
 
KeyValueParamsProviderReference - Class in org.anchoranalysis.bean.shared.params.keyvalue
 
KeyValueParamsProviderReference() - Constructor for class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
 
kurtosis(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics
 
Kurtosis - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
Kurtosis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis
 

L

l2norm() - Method in class org.anchoranalysis.spatial.point.Point3d
 
labelElements(Channel, List<T>, Optional<Map<Integer, T>>) - Method in class org.anchoranalysis.image.core.object.label.LabelObjects
Replaces the contents of the channel so that all element's voxels are labelled with successive unique integer identifiers 1,2,3 etc.
labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
 
labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
 
labelFor(ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
Determines a particular group-identifier for an input
labelFor(ImageCSVLabellerInitParams, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
 
labelFor(ImageLabellerStringMapInitParams<T>, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
 
labelFor(T, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
Determines a particular group-identifier for an input
labelForAggregation() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
A label to be used when aggregrating this annotation with others, or null if this makes no sense
LabelHeaders - Class in org.anchoranalysis.feature.io.results
Headers in a CSV file for the non-results (i.e.
LabelHeaders(String[]) - Constructor for class org.anchoranalysis.feature.io.results.LabelHeaders
Creates with only non-group headers
LabelHeaders(String[], String[]) - Constructor for class org.anchoranalysis.feature.io.results.LabelHeaders
 
LabelObjects<T> - Class in org.anchoranalysis.image.core.object.label
Writes a unique ID (successive integer IDs) for each elements's voxels into a channel, and 0 for background.
LabelObjects(Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class org.anchoranalysis.image.core.object.label.LabelObjects
 
LabelObjects(Optional<UnaryOperator<T>>, Optional<Consumer<OverlappingObject<T>>>, Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class org.anchoranalysis.image.core.object.label.LabelObjects
 
labels() - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
 
LanguageUtilities - Class in org.anchoranalysis.core.value
 
lastConnectedTo(ContourList) - Method in class org.anchoranalysis.plugin.points.contour.ContourList
 
LastDirectories - Class in org.anchoranalysis.plugin.io.bean.descriptivename
Derives a name by taking the filename together with optionally several subdirectories names.
LastDirectories() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
 
LastDirectories(int) - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
Creates for a particular number of subdirectories.
LastDirectoryAsPrefix - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
Looks for the last directory-name, and removes it in favour of using it as a prefix on a filename
LastDirectoryAsPrefix() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
 
lastIndex(String) - Method in class org.anchoranalysis.io.generator.sequence.SequenceMemory
 
lastIndexOf(Object) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
lastIndexOf(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
Launch - Class in org.anchoranalysis.launcher
A command-line interface used for launching experiments
LauncherConfig - Class in org.anchoranalysis.launcher.config
 
LauncherConfig() - Constructor for class org.anchoranalysis.launcher.config.LauncherConfig
 
LaunchInteractiveBrowser - Class in org.anchoranalysis.browser.launcher
Command-line application for launching the anchor GUI application, otherwise known as interactive-browser.
LazyEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store
Items are evaluated only when they are first needed.
LazyEvaluationStore(String) - Constructor for class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
 
leftSize() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
LegacyOutputEnabled - Class in org.anchoranalysis.plugin.mpp.experiment.bean.output
Deprecated.
Prefer another sub-class of OutputEnabledRules.
LegacyOutputEnabled() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
 
length() - Method in class org.anchoranalysis.feature.results.ResultsVector
 
length() - Method in class org.anchoranalysis.spatial.point.Vector3d
 
LessThan - Class in org.anchoranalysis.math.relation
 
LessThan() - Constructor for class org.anchoranalysis.math.relation.LessThan
 
LessThanBean - Class in org.anchoranalysis.bean.shared.relation
 
LessThanBean() - Constructor for class org.anchoranalysis.bean.shared.relation.LessThanBean
 
LessThanEqualTo - Class in org.anchoranalysis.math.relation
 
LessThanEqualTo() - Constructor for class org.anchoranalysis.math.relation.LessThanEqualTo
 
LessThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
 
LessThanEqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
 
LevelFromHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
Calculates a level (a threshold-value) from a histogram.
LevelFromHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
 
LevelPerObjectBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object
Creates a channel with a level calculated for each object variously
LevelPerObjectBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
 
LevelPerObjectIndependently - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object
Creates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.
LevelPerObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
 
LevelPerObjectNeighbors - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object
Calculates a threshold-level for each object collectively based on other objects
LevelPerObjectNeighbors() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
 
LevelResult - Class in org.anchoranalysis.plugin.image.intensity.level
 
LevelResult(int, ObjectMask, Histogram) - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResult
 
LevelResultCollection - Class in org.anchoranalysis.plugin.image.intensity.level
 
LevelResultCollection() - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
 
LevelResultCollectionFactory - Class in org.anchoranalysis.plugin.image.intensity.level
 
Limit<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
Limits the number of input-objects to a certain hard-maximum
Limit - Class in org.anchoranalysis.plugin.io.bean.provider.file
 
Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Limit
 
Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.Limit
 
LimitWithDirectory - Class in org.anchoranalysis.plugin.io.bean.provider.file
 
LimitWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
 
LinearLeastSquaresEllipseFitter - Class in org.anchoranalysis.plugin.points.bean.fitter
Fits a set of points to an ellipse using a linear least squares method.
LinearLeastSquaresEllipseFitter() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
 
LinearLeastSquaresEllipsoidFitter - Class in org.anchoranalysis.plugin.points.bean.fitter
Fits an ellipsoid to points using a linear least squares approach
LinearLeastSquaresEllipsoidFitter() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
 
LinearLeastSquaresViaNormalEquationBase - Class in org.anchoranalysis.plugin.points.bean.fitter
 
LinearLeastSquaresViaNormalEquationBase() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
 
LineBoundCalculator - Class in org.anchoranalysis.plugin.mpp.bean.bound
 
LineBoundCalculator() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
 
LinePlot<T extends IndexGetter> - Class in org.anchoranalysis.plot.index
A line graph with 1 or more series, with an index on the x-axis.
LinePlot(String, String[], LinePlot.YValGetter<T>) - Constructor for class org.anchoranalysis.plot.index.LinePlot
 
LinePlot.YValGetter<T> - Interface in org.anchoranalysis.plot.index
 
LineSegment - Class in org.anchoranalysis.mpp.mark.points
 
LineSegment() - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment
 
LineSegment(Point3i, Point3i) - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment
 
list() - Method in class org.anchoranalysis.bean.StringList
 
list() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
list() - Method in class org.anchoranalysis.spatial.box.BoundedList
The collection of element with bounding-boxes.
ListBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory
Factory for creating a java.util.List of Beans
ListBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.ListBeanFactory
 
ListBeanFactory(CreateFromList<T>) - Constructor for class org.anchoranalysis.bean.xml.factory.ListBeanFactory
 
ListBoundCalculator - Class in org.anchoranalysis.plugin.mpp.bean.bound
 
ListBoundCalculator() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.ListBoundCalculator
 
listFeatures() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
listFeaturesSubset(int, int) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
listFrom2i(Mask) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask
 
listFrom2i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
A list of two-dimensional integer points from the entire object-mask
listFrom3d(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
A list of points from the entire object-mask
listFrom3i(Mask) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask
 
listFrom3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
A list of three-dimensional integer points from the entire object-mask
listFromAllOutlines2i(ObjectCollection) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
A list of points as three-dimensional integers from the outline of all objects in a collection
listFromOutline2i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
A list of points as three-dimensional integers from the outline of an object-mask
listFromOutline3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
A list of points as three-dimensional integers from the outline of an object-mask
listFromSlicesInsideBox3i(Mask, BoundingBox, int, int) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask
 
listIterator() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
listIterator(int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
listOfBeans(String, HierarchicalConfiguration, Object) - Static method in class org.anchoranalysis.bean.xml.factory.HelperListUtilities
A list of instantiated bean objects from an XML configuration
listProbMap() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
ListSequence<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
Populates a FeatureListElem with references to other features formed by one or two sequences of integers, so that all the features of the following pattern are contained in the list.
ListSequence() - Constructor for class org.anchoranalysis.feature.bean.list.ListSequence
 
ListUpdatableMarkSetCollection - Class in org.anchoranalysis.mpp.feature.mark
 
ListUpdatableMarkSetCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
ListWithThumbnails<T,​S> - Class in org.anchoranalysis.plugin.image.feature.object
A list of items with an associated thumbnail-batch
ListWithThumbnails(List<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
 
ListWithThumbnails(List<T>, ThumbnailBatch<S>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
 
loadBean(Path) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader
Creates a bean by loading an XML description from the filesystem
loadBean(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader
Creates a bean by loading an XML description from the filesystem
loadBeanAssociatedXml(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader
Creates a bean by loading an XML description from the filesystem
loadBeanLocalized(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader
Creates a bean by loading an XML description from the filesystem
localise(Path) - Method in class org.anchoranalysis.bean.AnchorBean
Called once after the bean is created, localising the bean to a path on the filesystem.
localise(Path) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
localise(Path) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
LocalisedBeanException - Exception in org.anchoranalysis.bean.xml.error
Combines many exceptions into a single exception, searching for a Cause and creating message string, incorporating the other strings
LocalisedBeanException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
 
LocalSlices - Class in org.anchoranalysis.image.voxel.kernel
 
LocalSlices(int, int, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.LocalSlices
 
log(String) - Method in interface org.anchoranalysis.core.log.MessageLogger
 
log(String) - Method in class org.anchoranalysis.core.log.NullMessageLogger
 
log(String) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
 
log(String) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
 
log(String) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
 
log(String) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
 
log(String) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
 
Log4JReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
Log4JReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
 
logDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
 
logEnd(JobDescription, JobState, boolean) - Method in class org.anchoranalysis.experiment.task.processor.JobStartStopLogger
Performs logging for when a job ends.
logFormatted(String, Object...) - Method in interface org.anchoranalysis.core.log.MessageLogger
 
logFormatted(String, Object...) - Method in class org.anchoranalysis.core.log.NullMessageLogger
 
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
 
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
 
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
 
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
 
logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
 
Logger - Class in org.anchoranalysis.core.log
A logging-mechanism for both messages and errors.
Logger(MessageLogger) - Constructor for class org.anchoranalysis.core.log.Logger
Constructs with an error-reporter that writes into the message logger.
Logger(MessageLogger, ErrorReporter) - Constructor for class org.anchoranalysis.core.log.Logger
 
loggerForMonitor(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
 
LoggingDestination - Class in org.anchoranalysis.experiment.bean.log
The destination(s) to which log-messages are sent.
LoggingDestination() - Constructor for class org.anchoranalysis.experiment.bean.log.LoggingDestination
 
LoggingFixture - Class in org.anchoranalysis.test
Fixtures to create loggers that don't output anything
logGraphDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
 
logMemoryUsage(String, MessageLogger) - Static method in class org.anchoranalysis.core.system.MemoryUtilities
 
logStart(JobDescription) - Method in class org.anchoranalysis.experiment.task.processor.JobStartStopLogger
Performs logging for when a job starts.
LogUtilities - Class in org.anchoranalysis.core.log
 
LongestExtent - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
 
LongestExtent() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
 
LongestExtentWithin - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
 
LongestExtentWithin() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
LoopablePoints - Class in org.anchoranalysis.image.core.outline.traverser.visited
A set of points that can be looped, so as to form a path that ends with the same point that it begins with....
LoopablePoints(List<Point3i>, Point3i) - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
 
loopPointsLeft() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
 
loopPointsRight() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
 
lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
 
lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
 
lowerCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
Whether the count is less than a particular threshold.
LRUCache<K,​V> - Class in org.anchoranalysis.core.cache
A cache that discards items that haven't being used recently or frequently (as per Guava's size-based eviction's defaults)
LRUCache(int, CheckedFunction<K, V, E>) - Constructor for class org.anchoranalysis.core.cache.LRUCache
Constructor

M

main(String[]) - Static method in class org.anchoranalysis.browser.launcher.LaunchInteractiveBrowser
Entry point for command-line application
main(String[]) - Static method in class org.anchoranalysis.launcher.Launch
Entry point for command-line application
makeOutputPath(String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
Creates a full absolute path that completes the part of the path present in the outputter with an additional suffix.
makeOutputPath(String, String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
Like OutputterChecked.makeOutputPath(String) but additionally adds an extension.
makePathAbsolute(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
 
makePathAbsolute(String) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator
Generates a full path, given the final part (suffix) of a path.
makePathRelative(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
 
makePathRelative(Path) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator
Extracts a relative-file path, given the final part (suffix) of a path.
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
 
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
makeProposal(Optional<MarkCollection>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
 
makeProposal(Optional<MarksFromPartition>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelReplacePartition
 
makeProposal(Optional<MarksFromPartition>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
Calculates the Energy for a proposal
makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
 
makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
 
makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
 
makeRGBStack(Stack) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
 
makeSureConfigured() - Method in class org.anchoranalysis.io.bioformats.ConfigureBioformatsLogging
Makes sure logging is configured
Manifest - Class in org.anchoranalysis.io.manifest
A manifest for a particular experiment, that may refer to the outputs from particular jobs, each with their own manifest.
Manifest() - Constructor for class org.anchoranalysis.io.manifest.Manifest
 
MANIFEST_FUNCTION - Static variable in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
 
MANIFEST_FUNCTION - Static variable in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
 
manifestCouplingDefinition(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
ManifestCouplingDefinition - Class in org.anchoranalysis.plugin.io.manifest
 
ManifestCouplingDefinition() - Constructor for class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
 
ManifestDescription - Class in org.anchoranalysis.io.manifest
A description of an entry (e.g.
ManifestDescription(String, String) - Constructor for class org.anchoranalysis.io.manifest.ManifestDescription
 
ManifestDeserializer - Interface in org.anchoranalysis.io.manifest.deserializer
 
ManifestDirectoryDescription - Class in org.anchoranalysis.io.manifest
A description of an directory in the manifest.
ManifestDirectoryDescription(String, String, SequenceType<?>) - Constructor for class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
 
ManifestDirectoryDescription(Optional<ManifestDescription>, SequenceType<?>) - Constructor for class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
 
ManifestGenerator - Class in org.anchoranalysis.io.generator.combined
 
ManifestGenerator() - Constructor for class org.anchoranalysis.io.generator.combined.ManifestGenerator
 
map(Function<T, S>) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
Maps the existing object to another object, while retaining an identical confidence score.
map(UnaryOperator<ObjectMask>) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
Maps the underlying object-mask to another object-mask, reusing the same properties object.
map(Optional<S>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Like Optional.map(java.util.function.Function<? super T, ? extends U>) but tolerates an exception in the mapping function, which is immediately thrown.
map(Stream<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
Performs a Stream.map(java.util.function.Function<? super T, ? extends R>) but accepts a function that can throw a checked-exception
map(CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
Creates a new feature-list where each feature is the result of applying a map-function to an existing feature
map(CheckedFunction<ObjectMask, ObjectMask, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Creates a new ObjectCollection after mapping each item to another.
mapBoth(Optional<U>, Optional<V>, CheckedBiFunction<U, V, T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Mapping only occurs if both Optionals are non-empty (equivalent to a logical AND on the optionals)
mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Applies a function to map the bounding-box to a new-value (whose extent is expected to change in value)
mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Creates a new ObjectCollection after mapping the bounding-box on each object (while maybe changing the extent).
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value)
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Creates a new ObjectCollection after mapping the bounding-box on each object (whose extent should remain unchanged).
mapBoundingBoxPreserveExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value)
mapCalculator(UnaryOperator<FeatureCalculatorMulti<T>>) - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
 
mapChannel(CheckedUnaryOperator<Channel, OperationFailedException>) - Method in class org.anchoranalysis.image.core.stack.Stack
Produces a new stack with a particular mapping applied to each channel.
mapChannelIfSupported(int, BiFunction<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>, T>, Function<Channel, T>) - Method in class org.anchoranalysis.image.core.stack.ChannelMapper
 
mapChannelWithIndex(CheckedBiFunction<Channel, Integer, Channel, OperationFailedException>) - Method in class org.anchoranalysis.image.core.stack.Stack
Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available)
MapCreate<K,​V> - Class in org.anchoranalysis.core.identifier.name
A tree map that creates a new item, if it doesn't already exist, after a GET operation
MapCreate(Supplier<V>) - Constructor for class org.anchoranalysis.core.identifier.name.MapCreate
 
MapCreate(Supplier<V>, Comparator<K>) - Constructor for class org.anchoranalysis.core.identifier.name.MapCreate
 
mapFrom(Iterable<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a new feature-list by mapping an Iterable to Feature
mapFrom(Iterable<T>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by mapping an Iterable to ObjectMask
mapFromFiltered(Iterable<S>, Predicate<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a new feature-list by filtering an iterable and then mapping it to a feature
mapFromOptional(Iterable<T>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by mapping an Iterable to Optional
mapFromOptional(Iterator<T>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by mapping an Iterator to Optional
mapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by mapping integers (from a range) each to a ObjectMask
mapFromRange(int, int, IntFunction<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a new feature-list by mapping integers (from a range) each to a feature
mapFromRange(int, int, IntFunction<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection by mapping integers (from a range) each to a ObjectMask
mapFromRangeOptional(int, int, Class<? extends Exception>, CheckedIntFunction<Optional<Feature<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Creates a new feature-list by mapping integers (from a range) each to an optional feature
MapGroupToRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
Maps Group (String) to a CSVRow
MapGroupToRow() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.csv.MapGroupToRow
 
mapIntStream(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
Creates a new feature-list by mapping integers (from a range) each to an optional feature accepting a checked-exception
mapList(List<S>, ProgressReporter, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalProgress
Maps a list to new list, updating a progress-reporter for every element
mapListOptional(List<S>, ProgressReporter, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalProgress
Maps a list to a new list, including only certain items, updating a progress-reporter for every element
mapRangeToList(int, int, IntFunction<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Creates a list of elements, where each element corresponds to an index in a range.
mapToInt(Stream<S>, Class<? extends Exception>, CheckedToIntFunction<S, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
Performs a Stream.mapToInt(java.util.function.ToIntFunction<? super T>) but accepts a function that can throw a checked-exception.
mapToList(Collection<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Like FunctionalList.mapToList(Object[], Function) but tolerates exceptions in the mapping function.
mapToList(Collection<S>, Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Maps a collection to a list with each element derived from a corresponding element in the original collection.
mapToList(Stream<S>, Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Maps a stream to a list with each element derived from a corresponding element in the original collection.
mapToList(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Creates a new List after mapping each item to another type.
mapToList(S[], Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Like FunctionalList.mapToList(Object[], Function) but tolerates exceptions in the mapping function.
mapToList(S[], Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Maps an array to a list with each element derived from a corresponding element in the original array.
mapToListOptional(Collection<S>, Function<S, Optional<T>>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Maps a collection to a list with each element in the original collection maybe producing an element in the output
mapToListOptional(CheckedFunction<ObjectMask, Optional<T>, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Creates a new List after mapping each item to another (optional) type
mapToListWithIndex(List<S>, BiFunction<S, Integer, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Maps a collection to a list with each element derived from a corresponding element in the original collection - and also letting the map function use an index.
mapToObj(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
Performs a IntStream.mapToObj(java.util.function.IntFunction<? extends U>) but accepts a function that can throw a checked-exception.
mapToSortedSet(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Creates a new SortedSet after mapping each item to another type.
Mark - Class in org.anchoranalysis.mpp.mark
 
Mark() - Constructor for class org.anchoranalysis.mpp.mark.Mark
 
Mark(Mark) - Constructor for class org.anchoranalysis.mpp.mark.Mark
Copy constructor
MarkAnd(S, T) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
 
MarkAnnotationDeleter - Class in org.anchoranalysis.annotation.io.mark
 
MarkAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.mark.MarkAnnotationDeleter
 
MarkAnnotationReader<T> - Class in org.anchoranalysis.annotation.io.mark
Reads a DualMarksAnnotation from a path on the filesystem.
MarkAnnotationReader(boolean) - Constructor for class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
 
MarkAnnotationWriter<T> - Class in org.anchoranalysis.annotation.io.mark
 
MarkAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
 
markAsCompleted(boolean) - Method in class org.anchoranalysis.experiment.task.processor.JobState
 
markAsExecuting() - Method in class org.anchoranalysis.experiment.task.processor.JobState
 
markAsTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
 
MarkBounds - Class in org.anchoranalysis.mpp.bean.bound
 
MarkBounds() - Constructor for class org.anchoranalysis.mpp.bean.bound.MarkBounds
 
MarkBoundsDefine - Class in org.anchoranalysis.plugin.mpp.bean.bound
 
MarkBoundsDefine() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
 
MarkBoundsDefine(MarkBounds) - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
 
MarkBoundsProvider - Class in org.anchoranalysis.mpp.bean.provider
 
MarkBoundsProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkBoundsProvider
 
MarkBoundsReference - Class in org.anchoranalysis.plugin.mpp.bean.bound
 
MarkBoundsReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
 
MarkCollection - Class in org.anchoranalysis.mpp.mark
A collection of marks, termed a configuration in marked-point-processes academic literature.
MarkCollection() - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
 
MarkCollection(List<Mark>) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
 
MarkCollection(Stream<Mark>) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
 
MarkCollection(Mark) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
 
MarkCollectionDeserializer - Class in org.anchoranalysis.mpp.io.marks
 
MarkCollectionDeserializer() - Constructor for class org.anchoranalysis.mpp.io.marks.MarkCollectionDeserializer
 
MarkCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer
Proposes an entire collection (confguration) of marks
MarkCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer
 
MarkCollectionProvider - Class in org.anchoranalysis.mpp.bean.provider
Provides a collection of marks
MarkCollectionProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkCollectionProvider
 
MarkConicFactory - Class in org.anchoranalysis.mpp.mark.conic
 
MarkDistance - Class in org.anchoranalysis.mpp.bean.mark
 
MarkDistance() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkDistance
 
MarkDistanceAbstractPosition - Class in org.anchoranalysis.plugin.mpp.bean.distance
 
MarkDistanceAbstractPosition() - Constructor for class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceAbstractPosition
 
MarkDistanceRadii - Class in org.anchoranalysis.plugin.mpp.bean.distance
 
MarkDistanceRadii() - Constructor for class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceRadii
 
MarkEllipseCircumEstimate - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
Estimates the circumference of an ellipse based upon finding the area of the shell, and dividing // by the ShellRad
MarkEllipseCircumEstimate() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.MarkEllipseCircumEstimate
 
MarkEllipseFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
 
MarkEllipseFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
 
MarkEllipseSimple - Class in org.anchoranalysis.plugin.mpp.bean.proposer.split
 
MarkEllipseSimple() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
MarkEllipsoidFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
 
MarkEllipsoidFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
 
MarkEvaluator - Class in org.anchoranalysis.mpp.feature.bean.mark
 
MarkEvaluator() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
 
MarkFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
 
MarkFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory
 
markFactoryContext() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
MarkFactoryContext - Class in org.anchoranalysis.mpp.segment.kernel
 
MarkFactoryContext(MarkWithIdentifierFactory) - Constructor for class org.anchoranalysis.mpp.segment.kernel.MarkFactoryContext
 
MarkFromCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer
 
MarkFromCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer
 
MarkFromCollectionProposerUnary - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
 
MarkFromCollectionProposerUnary() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
 
MarkMergeProposer - Class in org.anchoranalysis.mpp.bean.proposer
 
MarkMergeProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
 
MarkMergeProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.merge
 
MarkMergeProposerReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
 
markNoProposal(ProposerFailureDescription) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
MarkPairCollection - Class in org.anchoranalysis.mpp.feature.mark
A pair collection where the underlying type is a simple IdentifiablePair
MarkPairCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.MarkPairCollection
 
MarkPointListFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
 
MarkPointListFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
 
MarkProposer - Class in org.anchoranalysis.mpp.bean.proposer
 
MarkProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkProposer
 
MarkProposerFromList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
MarkProposerFromList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
 
MarkProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
MarkProposerReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
 
MarkProposerStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
Annotates each image with a mark
MarkProposerStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
MarkProposerUnary - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
MarkProposerUnary() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
 
MarkProviderPointsFitterFromConvexHull - Class in org.anchoranalysis.plugin.points.bean.mark.provider.single
 
MarkProviderPointsFitterFromConvexHull() - Constructor for class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
MarkRegion - Class in org.anchoranalysis.mpp.bean.mark
 
MarkRegion() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkRegion
 
marks() - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks
The marks associated with the annotation
marks() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
 
marks() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
MARKS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories
Where collections of marks are typically placed in a define-experiment output
MarksAsUniqueValueGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
 
MarksAsUniqueValueGenerator(Dimensions, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
 
marksAt(Point3d, RegionMap, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
MarksComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer
 
MarksComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
 
marksDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
MarksFlattenedGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
 
MarksFlattenedGenerator(DrawObject, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksFlattenedGenerator
 
MarksFromEnergyHelper - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
 
marksFromMemo(MemoCollection) - Static method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MarksFromEnergyHelper
 
marksFromOverlays(ColoredOverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
 
marksFromOverlays(OverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
 
MarksFromPartition - Class in org.anchoranalysis.plugin.mpp.segment.optimization
A subset of a marks (as extracted during a partition)
MarksFromPartition(MarkCollection, PartitionedMarks) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
 
MarksGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
 
MarksGenerator(DrawObject, IdentifierGetter<Overlay>) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksGenerator
 
MarksGenerator(DrawObject, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksGenerator
 
MarksGeneratorBase - Class in org.anchoranalysis.mpp.io.marks.generator
 
MarksGeneratorBase(DrawOverlay, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
 
marksNew() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
 
MarkSplitProposer - Class in org.anchoranalysis.mpp.bean.proposer
 
MarkSplitProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer
 
MarkSplitProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.split
 
MarkSplitProposerReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
 
MarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
 
MarksWithDisplayStack(MarkCollection, DisplayStack) - Constructor for class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
 
MarksWithEnergyBreakdown - Class in org.anchoranalysis.mpp.feature.energy.marks
Marks with both the total energy and a breakdown by clique
MarksWithEnergyBreakdown(MarksWithTotalEnergy) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
MarksWithEnergyBreakdown(MarksWithTotalEnergy, EnergySavedInd, EnergySavedPairs, EnergySavedAll) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
MarksWithTotalEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks
A collection of marks with an associated (total) energy.
MarksWithTotalEnergy(MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
 
MarkWithIdentifierFactory - Class in org.anchoranalysis.mpp.bean.mark
 
MarkWithIdentifierFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
MarkWithIdentifierFactory(MarkFactory) - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
MarkWithPosition - Class in org.anchoranalysis.mpp.mark
 
MarkWithPosition() - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition
 
MarkWithPosition(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition
 
MarkWithPositionAndSingleRadius - Class in org.anchoranalysis.mpp.mark.conic
Base-class for a conic that has a single radius (circle, sphere etc.)
MarkWithPositionAndSingleRadius() - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
MarkWithPositionAndSingleRadius(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
Constructor with a bound on the radius
MarkWithPositionAndSingleRadius(MarkWithPositionAndSingleRadius) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
Copy constructor
mask(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
 
Mask - Class in org.anchoranalysis.image.core.mask
A channel that is restricted to two values (ON and OFF) so as to act like a mask.
Mask(Channel) - Constructor for class org.anchoranalysis.image.core.mask.Mask
Creates a mask from an existing channel using default values for OFF (0) and ON (255)
Mask(Channel, BinaryValues) - Constructor for class org.anchoranalysis.image.core.mask.Mask
Creates a mask from an existing channel
Mask(Dimensions, BinaryValues) - Constructor for class org.anchoranalysis.image.core.mask.Mask
Creates a new empty mask of particular dimensions and with particular binaryvalues
Mask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.core.mask.Mask
Creates a mask from an existing binary-voxels using default image resolution
Mask(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.mask.Mask
Creates a mask from an existing binary-voxels and a specific image resolution.
MaskAnd - Class in org.anchoranalysis.image.core.mask.combine
 
MaskAsSingleObject<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
Calculate a feature, treating a mask as a single-object on the energy-stack
MaskAsSingleObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
 
MaskComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer
 
MaskComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
 
MaskFactory - Class in org.anchoranalysis.image.core.mask
Helper routines to create new instances of Mask
MaskFromObjects - Class in org.anchoranalysis.image.core.mask
Creates a mask from one or more objects.
MaskIfHighLow - Class in org.anchoranalysis.image.core.mask.combine
 
MaskIntersectionAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
 
MaskIntersectionAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
 
MaskInverter - Class in org.anchoranalysis.image.core.mask
Inverts masks and objects
MaskOr - Class in org.anchoranalysis.image.core.mask.combine
 
MaskProvider - Class in org.anchoranalysis.image.bean.provider
 
MaskProvider() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProvider
 
MaskProviderUnary - Class in org.anchoranalysis.image.bean.provider
 
MaskProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProviderUnary
 
masks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
maskScaledXY(Dimensions, RegionMembershipWithFlags, BinaryValuesByte, double) - Method in class org.anchoranalysis.mpp.mark.Mark
 
MaskXor - Class in org.anchoranalysis.image.core.mask.combine
 
match(int, int) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
Helper method to record a matching between worker w and job j.
match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegEx
Returns an array of string components it matches successfully, or empty() if it cannot match
match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExList
 
match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
 
match(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
 
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
 
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
 
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
 
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
A predicate condition for an object to be kept in the collection
match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
 
match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
 
match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
 
Match - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
 
Match() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
 
matchDirectories() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
 
MatchedAppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
An append CSV and corresponding match value
MatchedAppendCsv() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
 
MatchedObject - Class in org.anchoranalysis.image.core.object
An object with associated matches.
MatchedObject(ObjectMask, ObjectCollection) - Constructor for class org.anchoranalysis.image.core.object.MatchedObject
 
MatcherIntersectionHelper - Class in org.anchoranalysis.plugin.image.bean.object.match
 
matchingFilesForDirectory(Path, InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
 
matchingFilesForDirectory(Path, InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
 
matchIntersectingObjects(ObjectCollection, ObjectCollection) - Static method in class org.anchoranalysis.plugin.image.bean.object.match.MatcherIntersectionHelper
 
max() - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
 
max(boolean) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
max(double) - Method in class org.anchoranalysis.spatial.point.Point3d
Element-wise maximum between this point and a scalar
max(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
Element-wise maximum between this point and a scalar
max(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
Element-wise maximum between this point and another
max(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Point3d
Element-wise maximum between this point and another
Max - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
Max() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Max
 
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
 
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType
 
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType
 
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType
 
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType
 
MAX_VALUE - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
 
MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType
 
MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType
 
maxAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Finds the maximum value of a function applied to each object in the collection.
MaxDensityKernel3 - Class in org.anchoranalysis.image.voxel.kernel.density
Erosion with a 3x3 or 3x3x3 kernel
MaxDensityKernel3(BinaryValuesByte, boolean, boolean, int) - Constructor for class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
 
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
 
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
 
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
 
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
 
maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
 
maxDistanceToClosestPoint(ContiguousVoxelPath, Point3i) - Static method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceToContiguousPath
The maximum-distance of a point to the closest point on the path
maxDistanceToHeadTail(ContiguousVoxelPath, Point3i) - Static method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceToContiguousPath
 
MaxFeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
1.
MaxFeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
 
Maximum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
The maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Maximum<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
 
Maximum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
 
Maximum() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Maximum
 
MAXIMUM - org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
 
MaximumIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
 
MaximumIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
 
MaximumNumberContourVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice
Maximum number of voxels on any slice's contour (edge voxels) across all slices.
MaximumNumberContourVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
 
MaximumNumberVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice
Maximum number of voxels in the object-mask across all slices.
MaximumNumberVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
 
MaxIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
 
MaxIntensity() - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
 
MaxIntensityBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer.max
The buffer used when making a maximum-intensity projection
MaxIntensityBuffer(Extent, VoxelsFactoryTypeBound<T>) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
 
MaxIntensityBufferByte - Class in org.anchoranalysis.image.voxel.buffer.max
 
MaxIntensityBufferByte(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferByte
 
MaxIntensityBufferFloat - Class in org.anchoranalysis.image.voxel.buffer.max
 
MaxIntensityBufferFloat(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferFloat
 
MaxIntensityBufferInt - Class in org.anchoranalysis.image.voxel.buffer.max
 
MaxIntensityBufferInt(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferInt
 
MaxIntensityBufferShort - Class in org.anchoranalysis.image.voxel.buffer.max
 
MaxIntensityBufferShort(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferShort
 
MaxIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram
 
MaxIntensityFromHistogram() - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
 
MaxIntensityProjectionPair - Class in org.anchoranalysis.mpp.overlap
 
MaxIntensityProjectionPair(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, RegionMembershipWithFlags, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.overlap.MaxIntensityProjectionPair
 
MaxNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
 
MaxNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.MaxNonZero
 
maxOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
MaxOverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
 
MaxOverlapRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
MaxOverlapRatio(double) - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
MaxRatioRadii - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
 
MaxRatioRadii() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.MaxRatioRadii
 
MaxSliceArea - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
MaxSliceArea() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MaxSliceArea
 
MaxTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
MaxTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxTwoChannels
 
maxValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
The maximum value this type can represent.
MaxWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
MaxWithConstant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
 
MaxWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
 
MaxWithConstant() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
 
maybeAddOutputs() - Method in class org.anchoranalysis.launcher.options.outputs.ProcessOutputOptions
Processes any options that have been defined to add/remove change the outputs that are enabled.
maybeAddPointToClosestEnd(Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
Adds the point to the closest end of the path....
maybeCreateUserFriendlyException(Throwable) - Static method in class org.anchoranalysis.bean.xml.error.HelperFriendlyExceptions
Possibly replaces an exception with a more user-friendly description
maybeDistanceCondition() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
 
maybeSubdirectory(Optional<String>, ManifestDirectoryDescription, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
Optionally creates a new context like with InputOutputContext.subdirectory(java.lang.String, org.anchoranalysis.io.manifest.ManifestDirectoryDescription, boolean) but only if a directory-name is defined
mean() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
mean() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
Calculates the mean
mean() - Method in class org.anchoranalysis.math.histogram.Histogram
 
mean() - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
 
mean() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
 
mean(double) - Method in class org.anchoranalysis.math.arithmetic.RunningSum
Calculates the mean
mean(double) - Method in class org.anchoranalysis.math.histogram.Histogram
calculates the mean after raising each histogram value to a power i.e.
mean(double, double) - Method in class org.anchoranalysis.math.histogram.Histogram
calculates the mean of (histogramVal - subtractVal)^power
Mean - Class in org.anchoranalysis.feature.bean.results
The mean of the results from a particular feature.
Mean - Class in org.anchoranalysis.image.feature.histogram
 
Mean<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
Arithmetic mean of a list of features
Mean() - Constructor for class org.anchoranalysis.feature.bean.results.Mean
 
Mean() - Constructor for class org.anchoranalysis.image.feature.histogram.Mean
 
Mean() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Mean
 
MeanAcrossObjects<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
Calculates the mean of a feature applied to each connected component
MeanAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
 
meanAndReset() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
Calculate the mean and then reset to zero
meanAndReset() - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection
Calculate the mean of each item and reset to zero.
meanExecutionTimeFailed() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
Mean execution-time of failed jobs in milliseconds.
meanExecutionTimeSuccess() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
Mean execution-time of successfully-completed jobs in milliseconds.
MeanFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
 
MeanFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.MeanFilter2D
 
MeanFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
 
MeanFromAll() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
 
MeanGeometric<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
 
MeanGeometric() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
 
meanGreaterEqualTo(int) - Method in class org.anchoranalysis.math.histogram.Histogram
 
MeanIntensityBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer.mean
 
MeanIntensityBuffer(VoxelsFactoryTypeBound<T>, Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
Simple constructor since no preprocessing is necessary.
MeanIntensityByteBuffer - Class in org.anchoranalysis.image.voxel.buffer.mean
 
MeanIntensityByteBuffer(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityByteBuffer
Simple constructor since no preprocessing is necessary.
MeanIntensityDifference - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
MeanIntensityDifference() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
 
MeanIntensityDifference(double) - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
 
MeanIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
 
MeanIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
 
MeanIntensityShortBuffer - Class in org.anchoranalysis.image.voxel.buffer.mean
 
MeanIntensityShortBuffer(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityShortBuffer
Simple constructor since no preprocessing is necessary.
meanNonZero() - Method in class org.anchoranalysis.math.histogram.Histogram
 
meanOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
MeanRaisedToPower - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
The mean of the intensity raised to power
MeanRaisedToPower() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
 
MeanThreeChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
Creates a new channel that is the mean of three input channels
MeanThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
 
meanXY() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
 
Median - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Applies a median-filter with square kernel
Median - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
Median() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
 
Median() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
 
MedianFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
 
MedianFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter2D
 
MedianFilter3D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
 
MedianFilter3D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D
 
membershipForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
membershipWithFlagsForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
MemoCollection - Class in org.anchoranalysis.mpp.feature.mark
A collection of memoized marks on which energies can be derived.
MemoCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
MemoCollection(EnergySavedInd, EnergyStackWithoutParams, MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
MemoCollection(MemoCollection) - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
MemoForIndex - Interface in org.anchoranalysis.mpp.mark.voxelized.memo
 
MemoList - Class in org.anchoranalysis.mpp.feature.mark
 
MemoList() - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoList
 
MemoryUsageReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
MemoryUsageReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
 
MemoryUtilities - Class in org.anchoranalysis.core.system
 
merge() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
Merges
merge(TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
 
merge(ObjectCollection) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger
Merges all the objects together that are found in a collection
merge(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger
Merges two objects together
MergeBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
A base class for algorithms that merge object-masks
MergeBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
 
MergeBase.MergeObjects - Interface in org.anchoranalysis.plugin.image.bean.object.provider.merge
 
mergeBoundingBoxes(Stream<ObjectMask>) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger
Merges all the bounding boxes of a stream of objects.
mergeBoundingBoxes(Stream<BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxMerger
Merges all the bounding boxes in a stream.
mergeBoundingBoxes(ObjectCollection) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger
Merges all the bounding boxes of a collection of objects.
MergeCandidate - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy
 
MergeCandidate(ContiguousVoxelPath, ContiguousVoxelPath, Point3i, Point3i) - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
 
Merged - Class in org.anchoranalysis.image.feature.bean.object.pair
Evaluates the first-object in a pair only
Merged() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged
 
Merged(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged
 
MERGED - org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
 
MergedPairsFeatures - Class in org.anchoranalysis.image.feature.session.merged
The list of features that can be used in a PairsTableCalculator
MergedPairsFeatures(FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
Creates to only calculate pair features.
MergedPairsFeatures(FeatureList<FeatureInputStack>, FeatureList<FeatureInputSingleObject>, FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
Creates with features for single, pair and image as a whole.
MergedPairsInclude - Class in org.anchoranalysis.image.feature.session.merged
 
MergedPairsInclude() - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
 
MergedPairsInclude(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
 
MergeGraph - Class in org.anchoranalysis.plugin.image.object.merge
A graph that stores each object as a vertex, where edges represent a neighborhood relation.
MergeGraph(PayloadCalculator, UpdatableBeforeCondition, Optional<UnitConverter>, AssignPriority, Logger, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.MergeGraph
Constructor
MergeGreedyToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
Naive greedy merge strategy when any two neighboring objects are merged if it increases a feature.
MergeGreedyToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
 
MergeLists - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
 
MergeLists() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
 
MergeMarkEllipse - Class in org.anchoranalysis.plugin.mpp.bean.proposer.merge
 
MergeMarkEllipse() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
 
mergeMultiplex(ObjectCollection, MergeBase.MergeObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
Merges either in a container, or altogether
mergeObjects(ObjectCollection) - Method in interface org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase.MergeObjects
 
MergePairs - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
Merges objects if a pair feature value satisfies a condition
MergePairs() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
 
MergeSpatialClusters - Class in org.anchoranalysis.plugin.ml.bean.cluster
Merges spatially-adjacent objects using the DBScan clustering algorithm.
MergeSpatialClusters() - Constructor for class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
 
MergeStrategy - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy
 
MergeStrategy(int) - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeStrategy
 
MergeToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
Merges neighboring objects if it results in an increase in the average feature-value calculated on each single object
MergeToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
 
MergeTwoCollectionsItemwise - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
Merges itemwise objects from two collections.
MergeTwoCollectionsItemwise() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
 
mergeViaZeroCheck(Channel, Channel, VoxelDataType, double) - Static method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
Creates a new channel which is a merged version of two input channels according to rules.
MergeWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
Base class for object-merging strategies that involve calculating a feature.
MergeWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
 
MergeWithOptionalDistanceConstraint - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
Expands MergeBase by optionally imposing a maximum-distance requirement between objects that are possibly merged.
MergeWithOptionalDistanceConstraint() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
 
messageLogger() - Method in class org.anchoranalysis.core.log.Logger
Where messages logged to
MessageLogger - Interface in org.anchoranalysis.core.log
Logs messages (strings) somewhere.
MessageLoggerList - Class in org.anchoranalysis.experiment.log
 
MessageLoggerList(Stream<StatefulMessageLogger>) - Constructor for class org.anchoranalysis.experiment.log.MessageLoggerList
 
metadataAggregated(NamedFeatureStore<FeatureInputResults>) - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
Derives metadata for the aggregated CSV output, if enabled.
metadataNonAggregated() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
Derives metadata for the non-aggregated CSV output.
MICRO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
 
midpoint() - Method in class org.anchoranalysis.spatial.box.BoundingBox
A mid-point in the bounding box, in the exact half way point between (crnr+extent)/2.
midPointBetween(Point3d, Point3d) - Static method in class org.anchoranalysis.spatial.point.Point3d
 
min() - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
 
min(boolean) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
min(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Point3d
Element-wise minimum between this point and another
min(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
Element-wise minimum between this point and another
min(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Point3d
Element-wise minimum between this point and another
Min - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
Min() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Min
 
MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
 
MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType
 
minArea() - Method in class org.anchoranalysis.mpp.overlap.MaxIntensityProjectionPair
 
minAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Finds the minimum value of a function applied to each object in the collection.
minDistanceMaxToHeadTail(Point3i, List<ContiguousVoxelPath>) - Static method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.FindMinimumDistance
The maximum-distance of a point to the closest contiguous-path
MinFeatureAsIndividual - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
 
MinFeatureAsIndividual() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.MinFeatureAsIndividual
 
MinFeatureIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
1.
MinFeatureIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
 
MinimaImposition - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
 
MinimaImposition() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition
 
MinimaImpositionGrayscaleReconstruction - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
 
MinimaImpositionGrayscaleReconstruction() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
 
MinimalExecutionTimeStatsReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
MinimalExecutionTimeStatsReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
 
Minimum - Class in org.anchoranalysis.image.feature.bean.object.pair
Ratio of first-object to second-object in a pair
Minimum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
The minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Minimum<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
 
Minimum() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum
 
Minimum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
 
Minimum() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Minimum
 
Minimum(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum
 
MINIMUM - org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
 
MinimumDistanceByDimension - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
The minimum distance in any one particular axis-aligned direction (i.e.
MinimumDistanceByDimension() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.MinimumDistanceByDimension
 
MinimumFilter - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider
 
MinimumFilter() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter
 
minNumPoints() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
 
minOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
MinTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
MinTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinTwoChannels
 
minVal - Variable in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
minValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
The minimum value this type can represent.
MinWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
MinWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
 
MockFeatureWithCalculation - Class in org.anchoranalysis.test.feature.plugins.mockfeature
A feature that returns the number-of-voxels in an object by using am internal mock-calculation.
MockFeatureWithCalculation() - Constructor for class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculation
 
MockFeatureWithCalculationFixture - Class in org.anchoranalysis.test.feature.plugins.mockfeature
Creates a mock-feature which used a mock FeatureCalculation under the hood
Mode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
Mode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
 
MonitoredSequentialExecutor<T> - Class in org.anchoranalysis.experiment.task.processor
Runs executes sequence of jobs/tasks/whatever monitoring various pieces of information - how many have run? - how many successful/failed? - how long did execution take? - etc.
MonitoredSequentialExecutor(Predicate<T>, Function<T, String>, Optional<MessageLogger>, boolean) - Constructor for class org.anchoranalysis.experiment.task.processor.MonitoredSequentialExecutor
 
MontageSlices - Class in org.anchoranalysis.plugin.imagej.bean.stack.provider
 
MontageSlices() - Constructor for class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
 
moreThanOneObj() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
Can more than one object exist?
moreThanOneObj() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
moreThanOneObj() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
 
MorphologicalDilation - Class in org.anchoranalysis.image.voxel.object.morphological
 
MorphologicalErosion - Class in org.anchoranalysis.image.voxel.object.morphological
 
MorphologicalIterations - Class in org.anchoranalysis.plugin.image.feature.bean.morphological
Specifies a certain number of iterations of the morphological operations of dilation and erosion
MorphologicalIterations() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
 
MorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider
Applies an ImageJ (2D) morphological operation to each slice
MorphologicalOperation() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
 
MorphologicalOperatorBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
Base class for performing morphological operations
MorphologicalOperatorBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
moveAcceptedToAvailable(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
 
moveAvailableToAccepted(Set<Mark>) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
 
MovieFromSlices - Class in org.anchoranalysis.plugin.image.task.bean.slice
 
MovieFromSlices() - Constructor for class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
MPPBean<T> - Class in org.anchoranalysis.mpp.bean
 
MPPBean() - Constructor for class org.anchoranalysis.mpp.bean.MPPBean
 
MPPInitParams - Class in org.anchoranalysis.mpp.bean.init
 
MPPInitParams(ImageInitParams, SharedObjects) - Constructor for class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
MPPInitParamsFactory - Class in org.anchoranalysis.mpp.io.input
 
MPPProvider<T,​S> - Class in org.anchoranalysis.mpp.bean.provider
 
MPPProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MPPProvider
 
Mser - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
Applies the MSER algorithm from imglib2
Mser() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
mult(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
multConstant(double) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
MultiBufferSized - Class in org.anchoranalysis.plugin.io.multifile.buffer
 
MultiBufferSized(Stack, SizeExtents) - Constructor for class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
 
MultiFileReader - Class in org.anchoranalysis.plugin.io.bean.stack.reader
 
MultiFileReader() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
 
MultiFileReaderOpenedRaster - Class in org.anchoranalysis.plugin.io.multifile
 
MultiFileReaderOpenedRaster(StackReader, ParsedFilePathBag) - Constructor for class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
MultiInput - Class in org.anchoranalysis.mpp.io.input
 
MultiInput(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput
 
MultiInput(ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput
 
MultiInputManager - Class in org.anchoranalysis.mpp.io.bean.input
 
MultiInputManager() - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
MultiInputManager(String, InputManager<? extends ProvidesStackInput>) - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
MultiInputManagerQuick - Class in org.anchoranalysis.plugin.quick.bean.input
A multi-input manager that makes various assumptions, so it can be more quickly specified.
MultiInputManagerQuick() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
 
MultiInputSubMap<T> - Interface in org.anchoranalysis.mpp.io.input
a sub-item of multi-input which: 1.
MultiLevelAnd - Class in org.anchoranalysis.io.output.enabled.multi
Outputs are enabled if they are contained in both of two MultiLevelOutputEnableds.
MultiLevelAnd(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
Creates using two MultiLevelOutputEnableds.
MultiLevelBinary - Class in org.anchoranalysis.io.output.enabled.multi
 
MultiLevelBinary(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
 
MultiLevelNot - Class in org.anchoranalysis.io.output.enabled.multi
The complement of an existing MultiLevelOutputEnabled where disabled outputs are enabled, and vice-versa.
MultiLevelNot(MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
 
MultiLevelOr - Class in org.anchoranalysis.io.output.enabled.multi
Outputs are enabled if they are contained in either of two MultiLevelOutputEnableds.
MultiLevelOr(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
Creates using two MultiLevelOutputEnableds.
MultiLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.multi
Whether an output is enabled or not in a context of hierarchy of different rules for outputting.
MultiLevelRecordedOutputs - Class in org.anchoranalysis.io.output.recorded
Like RecordedOutputs but accepts two levels, first and second, like in a MultiLevelRecordedOutputs.
MultiLevelRecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
 
MultiName - Interface in org.anchoranalysis.feature.io.name
A name that that uniquely identifies an entity, and is composed of two parts.
MultiNameFactory - Class in org.anchoranalysis.feature.io.name
Creates MultiName.
MultipleComparer - Class in org.anchoranalysis.annotation.io.bean.comparer
Allows comparison of an annotation with multiple other entities.
MultipleComparer() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
MultipleFileTypeGenerator<T> - Interface in org.anchoranalysis.io.generator
A Generator that creates multiple different file-types.
multipleProcessors(int, int) - Static method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
Creates a plan for a multiple CPU-processors
multipleSeries() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
multiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
Multiplexes between the selective and permissive writers based on a flag.
Multiply<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
Multiply() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
 
multiplyBy(double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic
Multiplies the value of all voxels by a factor
multiplyBy(ObjectMask, double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic
Multiplies each voxel by constant factor but only for voxels inside an object-mask
MultiplyByConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
MultiplyByConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
 
MultiplyByConstant(Feature<T>, double) - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
 
MultiplyConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
MultiplyConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
 
MultiplyTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
MultiplyTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyTwoChannels
 
MutableDirectory - Class in org.anchoranalysis.io.manifest.directory
An entry for a directory in the manifest, to which outputs and sub-directories can be later added.
MutableDirectory() - Constructor for class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
MutableDirectory(MutableDirectory) - Constructor for class org.anchoranalysis.io.manifest.directory.MutableDirectory
 

N

name() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
 
name() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
name() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
name() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
 
name() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
 
name() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
 
name() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
 
NamedBean<T extends AnchorBean<?>> - Class in org.anchoranalysis.bean
A bean with an associated textual name.
NamedBean() - Constructor for class org.anchoranalysis.bean.NamedBean
 
NamedBean(String, T) - Constructor for class org.anchoranalysis.bean.NamedBean
 
NamedChannel - Class in org.anchoranalysis.plugin.image.task.grouped
 
NamedChannel(String, Channel) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
 
NamedChannels - Class in org.anchoranalysis.plugin.io.bean.input.channel
An image viewed as a named set of channels
NamedChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
NamedChannelsAppend - Class in org.anchoranalysis.plugin.io.bean.input.channel
 
NamedChannelsAppend() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
NamedChannelsBase - Class in org.anchoranalysis.plugin.io.bean.input.channel
Parent for all the NamedChannels classes
NamedChannelsBase() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsBase
 
NamedChannelsQuick - Class in org.anchoranalysis.plugin.quick.bean.input
A particular type of NamedChannels which allows easier input of data, making several assumptions.
NamedChannelsQuick() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
 
NamedFeatureCalculateException - Exception in org.anchoranalysis.feature.calculate
A feature-calculation exception that occurs in a particular named feature, or else a general message of failure.
NamedFeatureCalculateException(Exception) - Constructor for exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException
Creates with a calculation error that doesn't pertain to any particular feature.
NamedFeatureCalculateException(String) - Constructor for exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException
Creates with a general failure message that doesn't pertain to any particular feature.
NamedFeatureCalculateException(String, String) - Constructor for exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException
Creates with a failure message associated with a particular feature.
NamedFeatureCalculatorMulti<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.evaluator
A FeatureCalculatorMulti with associated feature-names
NamedFeatureCalculatorMulti(FeatureCalculatorMulti<T>, FeatureNameList) - Constructor for class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
 
NamedFeatureStore<T extends FeatureInput> - Class in org.anchoranalysis.feature.list
 
NamedFeatureStore() - Constructor for class org.anchoranalysis.feature.list.NamedFeatureStore
 
NamedFeatureStoreFactory - Class in org.anchoranalysis.feature.list
 
NamedFiles - Class in org.anchoranalysis.plugin.io.bean.input.files
File-paths
NamedFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
 
NamedFiles(FilesProvider) - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
 
NamedPath - Class in org.anchoranalysis.io.output.path.prefixer
A path and associated name.
NamedPath(String, Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.NamedPath
 
NamedProvider<T> - Interface in org.anchoranalysis.core.identifier.provider
A collection of named-elements that provides an element for a given name.
NamedProviderBridge<S,​T> - Class in org.anchoranalysis.core.identifier.provider
 
NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>) - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
 
NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>, boolean) - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
 
NamedProviderCombine<T> - Class in org.anchoranalysis.core.identifier.provider
 
NamedProviderCombine() - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
 
NamedProviderGetException - Exception in org.anchoranalysis.core.identifier.provider
 
NamedProviderGetException(String, Throwable) - Constructor for exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
 
NamedProviderOutputter<T> - Class in org.anchoranalysis.io.generator.collection
Outputs entities from a NamedProvider into a directory using the names of each entity for a corresponding generated file.
NamedProviderOutputter(NamedProvider<T>, Generator<T>, OutputterChecked) - Constructor for class org.anchoranalysis.io.generator.collection.NamedProviderOutputter
 
NamedProviderStore<T> - Interface in org.anchoranalysis.core.identifier.provider.store
A provider, in which items can also be added.
NamedStacks - Class in org.anchoranalysis.image.core.stack
A set of image-stacks each with a name
NamedStacks() - Constructor for class org.anchoranalysis.image.core.stack.NamedStacks
 
NamedStacksSupplier - Interface in org.anchoranalysis.image.core.stack
 
NamedStacksUniformSize - Class in org.anchoranalysis.image.core.stack
Like a @{link NamedStacks but enforces a condition that all stacks must have the same dimensions
NamedStacksUniformSize() - Constructor for class org.anchoranalysis.image.core.stack.NamedStacksUniformSize
 
nameForPropValue(Double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
 
nameForPropValue(Double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
 
nameForPropValue(Integer) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
 
nameForPropValue(Integer) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
 
nameForPropValue(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
 
nameForPropValue(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
 
nameForPropValue(T) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty
Converts a particular value to a string representation
nameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
Constructs a full name from the output format string and an index
nameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
 
nameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
 
NameValue<T> - Interface in org.anchoranalysis.core.identifier.name
An object that has an associated textual name and value
NameValueSet<T> - Class in org.anchoranalysis.core.identifier.provider
 
NameValueSet() - Constructor for class org.anchoranalysis.core.identifier.provider.NameValueSet
 
NameValueSet(Iterable<? extends NameValue<T>>) - Constructor for class org.anchoranalysis.core.identifier.provider.NameValueSet
 
NANO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
 
negative() - Method in class org.anchoranalysis.image.core.orientation.Orientation
 
negative() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
negative() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
negative() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
negative() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
negative() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
NeighborGraph - Class in org.anchoranalysis.image.voxel.neighborhood
 
Neighborhood - Interface in org.anchoranalysis.image.voxel.neighborhood
 
NeighborhoodCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
A condition placed to determine if two objects could be potential neighbors are not (i.e.
NeighborhoodCondition(boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
 
NeighborhoodFactory - Class in org.anchoranalysis.image.voxel.neighborhood
Creates either a big voxel-neighborhood or a small voxel-neighborhood.
newlinesBeforeError() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
if true, then some extra newlines are inserted before error messages
newTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
next() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
 
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
 
nextIndex(int) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncomplete
 
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
 
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
 
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
 
nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
 
nextValue() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
 
NoAnnealing - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
 
NoAnnealing() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.annealing.NoAnnealing
 
noInterpolation() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
 
None - Class in org.anchoranalysis.image.bean.interpolator
 
None - Class in org.anchoranalysis.io.output.bean.enabled
No outputs are enabled.
None() - Constructor for class org.anchoranalysis.image.bean.interpolator.None
 
None() - Constructor for class org.anchoranalysis.io.output.bean.enabled.None
 
NONE - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
 
NoneExcept - Class in org.anchoranalysis.io.output.bean.rules
All outputs are disabled except particular ones.
NoneExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept
 
NoneExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept
Create with first-level output names
NonEmpty - Annotation Type in org.anchoranalysis.bean.annotation
Indicates that a collection must have at least one item.
nonExistingItem(String) - Static method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
 
nonExistingItem(String, String) - Static method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
 
NonMaximaSuppression<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
A strategy for reducing elements that greedily removes any element with a strong overlap with another.
NonMaximaSuppression() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
 
NonNegative - Annotation Type in org.anchoranalysis.bean.annotation
The bean-field should have a value >= 0
noOverlapWith(Mark, int) - Method in interface org.anchoranalysis.mpp.mark.QuickOverlapCalculation
A quick (computationally-efficient) test to see if we can reject the possibility of overlap
noPadding() - Method in class org.anchoranalysis.image.bean.spatial.Padding
 
normalisedRadii(Ellipsoid, Optional<Resolution>) - Static method in class org.anchoranalysis.mpp.mark.conic.EllipsoidUtilities
 
normalize() - Method in class org.anchoranalysis.spatial.point.Vector3d
 
NormalizeByConstant - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
NormalizeByConstant() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
 
NormalizeByMax - Class in org.anchoranalysis.plugin.image.feature.bean.score
This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
NormalizeByMax() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
 
NormalizeDifferenceToMedian - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Corrects a channel in the following way
NormalizeDifferenceToMedian() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
 
NormalizedPath - Class in org.anchoranalysis.plugin.io.bean.descriptivename
Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
NormalizedPath() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.NormalizedPath
 
NormalizedRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range.feature
The range of two feature values (i.e.
NormalizedRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.feature.NormalizedRange
 
NormalizeObjectIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
NormalizeObjectIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
 
NoSharedState - Class in org.anchoranalysis.experiment.task
Fake shared-state to use to indicate none exists (for type safety)
Not - Class in org.anchoranalysis.plugin.mpp.bean.check
 
Not() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.Not
 
NotFound<T> - Class in org.anchoranalysis.annotation.io.image.findable
A negative-result when an object is NOT found at a particular location.
NotFound(Path, String) - Constructor for class org.anchoranalysis.annotation.io.image.findable.NotFound
 
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.buffer.PredicateBufferBinary
Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary
Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed
Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset
Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary
Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary
Notifies the processor that there has been a change in slice (z global coordinate)
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint
Notifies the processor that there has been a change in z-coordinate
notifyChangeY(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint
Notifies the processor that there has been a change in y-coordinate
notifyChangeZ(int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor
Notifies the processor that there has been a change in z-coordinate
notifyChangeZ(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute
Notifies the processor that there has been a change in z-coordinate
notifyChangeZ(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
notifyChangeZ(int, int, UnsignedByteBuffer) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked
Notifies the processor that there has been a change in z-coordinate
notifyChangeZ(int, int, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
 
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
 
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
 
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
 
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
 
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
 
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
 
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
 
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
 
notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3NeighborMatchValue
 
NoTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer
Base class for ImageJRasterWriter that doesn't support writing time-series as a stack.
NoTimeSeries() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.NoTimeSeries
 
NotInContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
Filters objects to keep only those which are NOT in the container.
NotInContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
 
NotTouchingSceneBorder - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
Keeps only objects that are not adjacent to the scene-border (i.e.
NotTouchingSceneBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
 
NullInitParams - Class in org.anchoranalysis.bean.initializable.params
 
NullMessageLogger - Class in org.anchoranalysis.core.log
Does nothing with (i.e.
NullMessageLogger() - Constructor for class org.anchoranalysis.core.log.NullMessageLogger
 
NullParamsBean<T> - Class in org.anchoranalysis.bean
A base class for beans that require initialization but the initializations needs no parameters.
NullParamsBean() - Constructor for class org.anchoranalysis.bean.NullParamsBean
 
NullReporter<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
Dummy reporter that takes no action.
NullReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
 
NUMBER_DIGITS_IN_OUTPUT - Static variable in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
 
NUMBER_ELEMENTS_WRITTEN_ERRORED - Static variable in class org.anchoranalysis.io.output.writer.WriterRouterErrors
 
NUMBER_ELEMENTS_WRITTEN_NOT_ALLOWED - Static variable in class org.anchoranalysis.io.output.writer.CheckIfAllowed
 
numberBits() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
The number of bits required to represent a voxel.
numberBorderPixels(ObjectMask, OutlineKernelParameters) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
 
numberChannels() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
A list of channel-names or null if they are not available.
numberChannels() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
NumberChannels - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
 
NumberChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
 
numberCompletedFailed() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
 
numberCompletedFailureJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
numberCompletedJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
numberCompletedSuccess() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
 
numberCompletedSuccessfullyJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.Orientation
 
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.Mark
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle2D
 
numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle3D
 
numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAxisAngle
 
numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory
The dimensionality of the rotation-matrix.
numberDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
Number of output-names that were not enabled.
NumberDistinctValues - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
NumberDistinctValues() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
 
numberEdges() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
The number of edges in the graph.
numberEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
Number of output-names that were enabled.
numberExecutingJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
numberFoundFrom(Set<Contour>) - Method in class org.anchoranalysis.plugin.points.contour.ContourList
 
numberFrames() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
 
numberFrames() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
numberFrames() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
 
numberFrames() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
numberGPUs() - Method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
 
numberImageFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
 
NumberIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
 
NumberIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
 
NumberIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
1.
NumberIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
 
numberItemsCurrentlyStored() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
Number of items currently stored in cache
NumberIterations - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
 
NumberIterations() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
 
NumberIterations(int) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
 
numberManifests() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
 
NumberMarks - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
 
NumberMarks - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
 
NumberMarks() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.collection.NumberMarks
 
NumberMarks() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.NumberMarks
 
NumberMarksFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
 
NumberMarksFromManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
 
numberMatches() - Method in class org.anchoranalysis.image.core.object.MatchedObject
 
NumberNeighboringVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
Calculates the number of voxels on the object that have a neighbor (according to a binary-mask on an energy-channel)
NumberNeighboringVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
 
numberNonNullConverters() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
numberNotCompleted() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
Number of jobs that have not been completed.
NumberObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.collection
 
NumberObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
 
numberOngoingJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
numberPaired() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
 
numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
 
numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
numberPairFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
 
NumberPoints - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
 
NumberPoints() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.NumberPoints
 
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
numberRegions() - Method in class org.anchoranalysis.mpp.mark.Mark
 
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
NumberRemovedVoxelsAfterClosing - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
How many pixels are removed after a morphological closing operation on the object-mask.
NumberRemovedVoxelsAfterClosing() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
 
numberSeries() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
 
numberSeries() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
numberSingleFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
 
numberSlicesProcessed() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
 
numberTotalScheduledJobs() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
Total number of scheduled jobs.
numberUnassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
 
numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
 
numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
numberUniqueColors() - Method in interface org.anchoranalysis.core.color.ColorIndex
 
numberUniqueColors() - Method in class org.anchoranalysis.core.color.ColorIndexModulo
 
numberUniqueColors() - Method in class org.anchoranalysis.core.color.ColorList
 
numberUniqueColors() - Method in class org.anchoranalysis.core.color.SingleColor
 
numberVertices() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
The number of vertices in the graph.
numberVoxels() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
 
NumberVoxels - Class in org.anchoranalysis.image.feature.bean.object.single
 
NumberVoxels() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
 
NumberVoxelsAtBorder - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
 
NumberVoxelsAtBorder() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
 
numberVoxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
The number of "ON" voxels on the object-mask
numFrames() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
 
numGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
 
numImagesAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
numImagesTotal() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
numImagesWithAcceptedAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
numImagesWithoutAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
numImagesWithSkippedAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
numProbMap() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
numRegions() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
numSlices() - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
 
numSlices() - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
 
numSlices() - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
 
numSlices() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
 
NumTouchingVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
A scheme for counting the touching voxels by intersection of object-masks
NumTouchingVoxelFaces() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxelFaces
 
NumTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
A scheme for counting touching voxels.
NumTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxels
 
numUnassignedLeft() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
numUnassignedRight() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 

O

ObjectAggregationBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
Calculates a feature for a set of objects using this stack as a energy-stack, and aggregates.
ObjectAggregationBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
 
ObjectAsPoints - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
ObjectAsPoints() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
 
ObjectCollection - Class in org.anchoranalysis.image.voxel.object
A collection of ObjectMask
ObjectCollection() - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection
Creates with no objects
ObjectCollection(Stream<ObjectMask>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection
Creates with elements from a stream
ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object.factory
Creates ObjectCollection using various utility and helper methods
ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider
 
ObjectCollectionProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProvider
 
ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
 
ObjectCollectionProviderFilterBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
 
ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
 
ObjectCollectionProviderMorphological() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
 
ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider
Base class for ObjectCollectionProvider that take a objects bean-field of same type as provided.
ObjectCollectionProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
 
ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
 
ObjectCollectionProviderWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
 
ObjectCollectionRTree - Class in org.anchoranalysis.image.voxel.object
An R-Tree of object-masks (indexed via a derived bounding-box).
ObjectCollectionRTree(ObjectCollection) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
Creates an r-tree for particular objects.
ObjectCollectionWithProperties - Class in org.anchoranalysis.image.core.object.properties
Like an ObjectCollection but each object has associated properties.
ObjectCollectionWithProperties() - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
ObjectCollectionWithProperties(Stream<ObjectWithProperties>) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
ObjectCollectionWithProperties(ObjectCollection) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
ObjectCollectionWithProperties(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
ObjectCollectionWithPropertiesFactory - Class in org.anchoranalysis.image.core.object.properties
 
ObjectComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer
An object-collection to be used to compare against something
ObjectComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
 
objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
Copies an area corresponding to an object-mask to another Voxels
ObjectDrawAttributes - Class in org.anchoranalysis.overlay.writer
A means of extracting attributes associated with a particular object (e.g.
ObjectDrawAttributes(ColorIndex) - Constructor for class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
Creates with a specific color-index and uses the iteration-index as both the ID and color-ID
ObjectDrawAttributes(ColorIndex, IdentifierGetter<ObjectWithProperties>, IdentifierGetter<ObjectWithProperties>) - Constructor for class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
 
ObjectDrawAttributesFactory - Class in org.anchoranalysis.overlay.writer
 
ObjectFilter - Class in org.anchoranalysis.image.bean.object
 
ObjectFilter() - Constructor for class org.anchoranalysis.image.bean.object.ObjectFilter
 
ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
A filter that combines other filters (in a list)
ObjectFilterCombine() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine
 
ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter
Uses a predicate to make a decision whether to keep objects or not.
ObjectFilterPredicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
 
ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter
An independent object-filter that uses a relation in its predicate.
ObjectFilterRelation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
 
objectFor(T) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
An object-mask for a given element.
ObjectInputStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize
 
ObjectInputStreamDeserializer() - Constructor for class org.anchoranalysis.core.serialize.ObjectInputStreamDeserializer
 
ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object
 
ObjectMask - Class in org.anchoranalysis.image.voxel.object
An object expressed in voxels, bounded within overall space.
ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
 
ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
Creates an object-mask to correspond to bounded-voxels.
ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
 
ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
Creates an object-mask with a corner at the origin (i.e.
ObjectMask(BoundingBox) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
Creates an object-mask to corresponding to a bounding-box with all pixels off (0)
ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
 
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
 
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
 
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
 
ObjectMaskMerger - Class in org.anchoranalysis.image.core.merge
Merges one or more ObjectMasks into a single object
ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object
A custom "stream" like class for various functional-programming operations on ObjectCollection
ObjectMaskStream(ObjectCollection) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMaskStream
 
ObjectMatcher - Class in org.anchoranalysis.image.bean.object
Matches an object with other objects.
ObjectMatcher() - Constructor for class org.anchoranalysis.image.bean.object.ObjectMatcher
 
ObjectOutputStreamGenerator<T extends Serializable> - Class in org.anchoranalysis.io.generator.serialized
 
ObjectOutputStreamGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
 
ObjectOutputStreamGenerator(Optional<String>) - Constructor for class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
 
ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
 
ObjectRadiusStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
 
objects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
objects() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
All objects stored in the r-tree (whose order corresponds to indices in delegate
objects() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
objects(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
 
OBJECTS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories
Where collections of objects are typically placed in a define-experiment output
objectsAreAllInside(Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
ObjectSerializerPeriodicReporter<T extends Serializable> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
ObjectSerializerPeriodicReporter(String) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
 
objectsForThumbnail(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
 
objectsForThumbnail(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
 
objectsForThumbnail(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
Selects objects from an input that will be used for thumbnail generation
ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.object.factory
Creates a ObjectCollection from the connected-components of a mask or binary-voxels.
ObjectsFromConnectedComponentsFactory() - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
 
ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
 
ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
 
ObjectsFromConnectedComponentsFactory(int) - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
 
objectsFromOverlays(OverlayCollection) - Static method in class org.anchoranalysis.overlay.collection.OverlayCollectionObjectFactory
Creates objects from whatever Overlays are found in the collection *
ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison
 
ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
 
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
The objects to draw (without any colors) on the background
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
 
objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
 
ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge
A vertex in a merge graph representing an object (and and an associated payload)
ObjectVertex(ObjectMask, double) - Constructor for class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
 
ObjectWithEllipse - Class in org.anchoranalysis.plugin.points.calculate.ellipse
 
ObjectWithEllipse(ObjectMask, Ellipse) - Constructor for class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
 
ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
Finds the object with the maximum feature-value from a collection.
ObjectWithMaximumFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
 
ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
Finds the object with the maximum feature among a group of matches for each object.
ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
 
ObjectWithProperties - Class in org.anchoranalysis.image.core.object.properties
An ObjectMask with associated key-value properties.
ObjectWithProperties(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
ObjectWithProperties(ObjectMask, Map<String, Object>) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
ObjectWithProperties(BoundingBox) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
obtain(int, AggregateReceiver<T>, PeriodTriggerBank<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
 
obtain(int, PeriodReceiver<S>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
 
of(boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborhoodFactory
Gets an appropriate neighborhood
of(boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.SelectDimensionsFactory
 
of(boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.SelectDimensionsFactory
 
of(Collection<ObjectMask>...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection with elements copied from existing collections
of(Optional<ObjectCollection>...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection with elements copied from existing collections (if they exist)
of(Stream<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
Creates a list from a stream.
of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
 
of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
 
of(CalculationResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
 
of(SessionInput<FeatureInputSingleObject>, boolean) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
 
of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection with elements from the parameter-list of BinaryVoxels converting the voxels in their entireity to an object-mask at the origin.
of(ObjectCollection...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection with elements copied from existing collections
of(ObjectMask...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
Creates a new collection with elements from the parameter-list
offset(int, int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
offset(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
offset(int, int) - Method in class org.anchoranalysis.spatial.Extent
Calculates a XY-offset of a point in a buffer whose dimensions are this extent
offset(int, int, int) - Method in class org.anchoranalysis.spatial.Extent
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
offset(Point2i) - Method in class org.anchoranalysis.spatial.Extent
Calculates a XY-offset of a point in a buffer whose dimensions are this extent
offset(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
offset(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
offsetGlobal(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
offsetRelative(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
offsetSlice(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
offsetSlice(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
Calculates a XY-offset of a point in a buffer whose dimensions are this extent
OffsettedPointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
Like a PointTwoDimensionalConsumer but also has a buffer offset.
OffsettedScalarTwoDimensionalConsumer<E extends Exception> - Interface in org.anchoranalysis.spatial.point.consumer
Like a ScalarTwoDimensionalConsumer but accepts two coordinates of a point and an offset value.
ofResolved(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
 
OMETiff - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
Writes a stack to the filesystem as a OME-XML using the Bioformats library.
OMETiff() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMETiff
 
OMEXML - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
Writes a stack to the filesystem as a OME-XML using the Bioformats library.
OMEXML() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMEXML
 
One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
Selects one specific channel from a set of stacks
One() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
 
oneOnly(String, String, boolean, boolean) - Static method in class org.anchoranalysis.bean.initializable.CheckMisconfigured
Checks that one of two properties is defined, but not both simultaneously (exclusive OR).
OneStageGenerator<T> - Class in org.anchoranalysis.io.generator
 
OneStageGenerator() - Constructor for class org.anchoranalysis.io.generator.OneStageGenerator
 
ongoingTasksLessThan(int) - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
 
onInit() - Method in class org.anchoranalysis.bean.NullParamsBean
As there's no parameters we expose a different method
onInit() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
onInit(NullInitParams) - Method in class org.anchoranalysis.bean.NullParamsBean
 
onInit(KeyValueParamsInitParams) - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
 
onInit(FeatureInitParams) - Method in class org.anchoranalysis.feature.bean.Feature
Called after initialization.
onInit(SharedFeaturesInitParams) - Method in class org.anchoranalysis.feature.bean.list.ReferencedFeatures
 
onInit(SharedFeaturesInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
 
onInit(ImageInitParams) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
 
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
 
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
 
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
 
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
 
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
 
onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
 
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
 
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
 
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
 
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
 
onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
onInit(PointsInitParams) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
 
onInit(P) - Method in class org.anchoranalysis.bean.initializable.InitializableBean
Called after initialization.
OnlyIf - Class in org.anchoranalysis.experiment.bean.log
Logs messages to a particular location ONLY if certain conditions are fulfilled.
OnlyIf() - Constructor for class org.anchoranalysis.experiment.bean.log.OnlyIf
 
open() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
 
open() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
 
open() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
 
open() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
 
open() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
 
open(int, ProgressReporter) - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
 
open(int, ProgressReporter) - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
 
OpenCVWriter - Class in org.anchoranalysis.plugin.opencv.bean.writer
Writes a stack to the filesystem using OpenCV and a specified extension.
OpenCVWriter() - Constructor for class org.anchoranalysis.plugin.opencv.bean.writer.OpenCVWriter
 
openFile(Path) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
 
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
 
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
 
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
 
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
 
openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
openMarksFromFilePath(Path) - Static method in class org.anchoranalysis.test.experiment.TestLoaderMPP
 
openMarksFromTestPath(String) - Method in class org.anchoranalysis.test.experiment.TestLoaderMPP
 
openXmlAbsoluteFilePath(String) - Static method in class org.anchoranalysis.test.TestLoader
Opens a XML document - with an absolute path on the filesystem
openXmlAbsoluteFilePath(Path) - Static method in class org.anchoranalysis.test.TestLoader
Opens a XML document - with an absolute path on the filesystem
openXmlFromTestPath(String) - Method in class org.anchoranalysis.test.TestLoader
Opens a XML document - with a path relative to the test root
OperationFailedException - Exception in org.anchoranalysis.core.exception
 
OperationFailedException(String) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedException
 
OperationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedException
 
OperationFailedException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedException
 
OperationFailedRuntimeException - Exception in org.anchoranalysis.core.exception
 
OperationFailedRuntimeException(Exception) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedRuntimeException
 
OperationFailedRuntimeException(String) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedRuntimeException
 
OperationMap<T> - Class in org.anchoranalysis.mpp.io.input
Stores objects as operations
OperationMap() - Constructor for class org.anchoranalysis.mpp.io.input.OperationMap
 
OptimizationContext - Class in org.anchoranalysis.mpp.segment.optimization
 
OptimizationContext(String, EnergySchemeWithSharedFeatures, DualStack, TriggerTerminationCondition, InputOutputContext, RandomNumberGenerator, MarkWithIdentifierFactory) - Constructor for class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
 
OptimizationScheme<S,​U> - Class in org.anchoranalysis.mpp.segment.bean.optimization
An optimization-scheme that uses kernels to make changes to state
OptimizationScheme() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.OptimizationScheme
 
OptimizationStep<S,​T> - Class in org.anchoranalysis.mpp.segment.optimization.step
 
OptimizationStep() - Constructor for class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
OptimizationStepLogReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
OptimizationStepLogReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
 
OptimizationTerminatedEarlyException - Exception in org.anchoranalysis.mpp.segment.optimization
 
OptimizationTerminatedEarlyException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.OptimizationTerminatedEarlyException
 
OptionalBean - Annotation Type in org.anchoranalysis.bean.annotation
Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must always have a non-null value.
OptionalFactory - Class in org.anchoranalysis.bean
Utility functions to create Optional from nullable providers or boolean flags.
OptionalNameValue<V> - Class in org.anchoranalysis.io.generator.combined
A simple container expressing a value and an associationed optional name.
OptionalNameValue(Optional<String>, V) - Constructor for class org.anchoranalysis.io.generator.combined.OptionalNameValue
 
OptionalOperationUnsupportedException - Exception in org.anchoranalysis.core.exception
 
OptionalOperationUnsupportedException() - Constructor for exception org.anchoranalysis.core.exception.OptionalOperationUnsupportedException
 
OptionalOperationUnsupportedException(Exception) - Constructor for exception org.anchoranalysis.core.exception.OptionalOperationUnsupportedException
 
OptionalOperationUnsupportedException(String) - Constructor for exception org.anchoranalysis.core.exception.OptionalOperationUnsupportedException
 
OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer
 
OptionalUtilities - Class in org.anchoranalysis.core.functional
Additional utility functions for Optional and exceptions.
Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
Applies multiples filter with logical OR i.e.
Or() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
 
Or() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
 
order(String) - Method in interface org.anchoranalysis.core.index.bounded.OrderProvider
 
OrderedFeatureList<T extends FeatureInput> - Interface in org.anchoranalysis.mpp.feature.addcriteria
 
OrderedList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
OrderedList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrderedList
 
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
 
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
 
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
 
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
 
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
 
orderedListOfFeatures() - Method in interface org.anchoranalysis.mpp.feature.addcriteria.OrderedFeatureList
A list of features used to determine the add-criteria, or null if irrelevant.
orderedListOfFeatures() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
 
orderedListOfFeatures() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
 
OrderedRadius - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
 
OrderedRadius() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
 
OrderProvider - Interface in org.anchoranalysis.core.index.bounded
 
orElseGet(Optional<T>, CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
Like Optional.orElseGet(java.util.function.Supplier<? extends T>) but tolerates an exception in the supplier function, which is immediately thrown.
orFlat(Optional<T>...) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
The first optional if it's present, or the second, or the third etc.
org.anchoranalysis.annotation - package org.anchoranalysis.annotation
Ground truth for an image in diverse forms.
org.anchoranalysis.annotation.image - package org.anchoranalysis.annotation.image
Annotations that apply to an image as a whole.
org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io
Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment
A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator
Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean
Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer
What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image
Reading and writing whole-image label annotations.
org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable
The outcome of searching for annotations or images on the file-system.
org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark
Reading and writing annotations basedupon marks to the file-system.
org.anchoranalysis.annotation.mark - package org.anchoranalysis.annotation.mark
Annotations that use one or more marks to describe entities in an image.
org.anchoranalysis.bean - package org.anchoranalysis.bean
Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.annotation - package org.anchoranalysis.bean.annotation
Annotations that decorate fields in an Anchor Bean.
org.anchoranalysis.bean.define - package org.anchoranalysis.bean.define
Define and related-classes.
org.anchoranalysis.bean.define.adder - package org.anchoranalysis.bean.define.adder
DefineAdder and related-classes.
org.anchoranalysis.bean.error - package org.anchoranalysis.bean.error
Exceptions that can occur executing generic operations on Anchor Beans.
org.anchoranalysis.bean.initializable - package org.anchoranalysis.bean.initializable
Initializing beans with particular parameters, including recursively.
org.anchoranalysis.bean.initializable.params - package org.anchoranalysis.bean.initializable.params
Some kinds of parameters used when initializing beans.
org.anchoranalysis.bean.initializable.property - package org.anchoranalysis.bean.initializable.property
Performing initializion on particular properties in a bean.
org.anchoranalysis.bean.permute - package org.anchoranalysis.bean.permute
Applying permutations to a bean's fields.
org.anchoranalysis.bean.permute.property - package org.anchoranalysis.bean.permute.property
Applying permutations to the properties of a bean.
org.anchoranalysis.bean.permute.setter - package org.anchoranalysis.bean.permute.setter
Setter used to impose a permutation on bean properties.
org.anchoranalysis.bean.provider - package org.anchoranalysis.bean.provider
A means of creating / loading / referencing a bean from another bean or class.
org.anchoranalysis.bean.shared - package org.anchoranalysis.bean.shared
Utility beans which have a generally broader use than a specific module.
org.anchoranalysis.bean.shared.color - package org.anchoranalysis.bean.shared.color
Beans that specify colors.
org.anchoranalysis.bean.shared.color.scheme - package org.anchoranalysis.bean.shared.color.scheme
Beans that create lists or indices of colors according to particular schemes.
org.anchoranalysis.bean.shared.params - package org.anchoranalysis.bean.shared.params
Setting, referencing and initializing key-value parameters.
org.anchoranalysis.bean.shared.params.keyvalue - package org.anchoranalysis.bean.shared.params.keyvalue
Referencing a particular KeyValueParams.
org.anchoranalysis.bean.shared.path - package org.anchoranalysis.bean.shared.path
Defines a root path directory on the filesystem whre files are read / written.
org.anchoranalysis.bean.shared.random - package org.anchoranalysis.bean.shared.random
Specifies a particular type of random-number generator.
org.anchoranalysis.bean.shared.regex - package org.anchoranalysis.bean.shared.regex
Specifies regular-expressions.
org.anchoranalysis.bean.shared.relation - package org.anchoranalysis.bean.shared.relation
Specifies a binary relation of some kind between scalars.
org.anchoranalysis.bean.shared.relation.threshold - package org.anchoranalysis.bean.shared.relation.threshold
Specifies a unary relation to a *threshold* value.
org.anchoranalysis.bean.store - package org.anchoranalysis.bean.store
Adding beans to collections.
org.anchoranalysis.bean.xml - package org.anchoranalysis.bean.xml
Reading Beans from XML files.
org.anchoranalysis.bean.xml.error - package org.anchoranalysis.bean.xml.error
Exceptions that can thrown when loading beans from XML.
org.anchoranalysis.bean.xml.factory - package org.anchoranalysis.bean.xml.factory
Custom factories for loading beans in custom ways from XML.
org.anchoranalysis.browser.launcher - package org.anchoranalysis.browser.launcher
Launching the anchor GUI interactive application from command-line.
org.anchoranalysis.core.cache - package org.anchoranalysis.core.cache
Caching (memozing) calls to a method so an operation does not need to be repeated.
org.anchoranalysis.core.color - package org.anchoranalysis.core.color
Specifying particular colors and groups of colors.
org.anchoranalysis.core.concurrency - package org.anchoranalysis.core.concurrency
Specifying how many CPUs and GPUs can be allocated for some purpose.
org.anchoranalysis.core.exception - package org.anchoranalysis.core.exception
Very general exceptions and base classes for exceptions with wide applicability.
org.anchoranalysis.core.exception.combinable - package org.anchoranalysis.core.exception.combinable
Nested exceptions of similar type that can be combined together in a summary.
org.anchoranalysis.core.exception.friendly - package org.anchoranalysis.core.exception.friendly
Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly error descriptions.
org.anchoranalysis.core.functional - package org.anchoranalysis.core.functional
Utilities and interfaces for applying functional-programming.
org.anchoranalysis.core.functional.checked - package org.anchoranalysis.core.functional.checked
Versions of many functional-interfaces in java.util.function that throw checked-exceptions.
org.anchoranalysis.core.graph - package org.anchoranalysis.core.graph
Data-structures for directed and undirected graphs, with or without an edge payload.
org.anchoranalysis.core.identifier.getter - package org.anchoranalysis.core.identifier.getter
Data structures for adding a unique name (a String or integer identifier) to other entities.
org.anchoranalysis.core.identifier.name - package org.anchoranalysis.core.identifier.name
Data structures for name (String) and value associations.
org.anchoranalysis.core.identifier.provider - package org.anchoranalysis.core.identifier.provider
A collection of named-elements, a NamedProvider, and related operations.
org.anchoranalysis.core.identifier.provider.store - package org.anchoranalysis.core.identifier.provider.store
Data structures like NamedProvider with supporting for adding new elements.
org.anchoranalysis.core.index - package org.anchoranalysis.core.index
Classes to support getting/setting/specifying unique-integers (indices) for elements.
org.anchoranalysis.core.index.bounded - package org.anchoranalysis.core.index.bounded
A range of elements with indiced, bounded to lie between particular a minimum and maximum.
org.anchoranalysis.core.index.bounded.bridge - package org.anchoranalysis.core.index.bounded.bridge
Exposes one type as a BoundedIndexContainer of another type.
org.anchoranalysis.core.log - package org.anchoranalysis.core.log
Interfaces to log messages, both information and error messages.
org.anchoranalysis.core.log.error - package org.anchoranalysis.core.log.error
Mechanism for reporting errors (exceptions/throwables) to the user.
org.anchoranalysis.core.progress - package org.anchoranalysis.core.progress
Classes to allow for tracking the progress of a task that can be broken into smaller units, for reporting to the user.
org.anchoranalysis.core.random - package org.anchoranalysis.core.random
Generating random numbers.
org.anchoranalysis.core.serialize - package org.anchoranalysis.core.serialize
Utilities for serializing and deserializing objects.
org.anchoranalysis.core.system - package org.anchoranalysis.core.system
Utilities for interacting with the operating system or computer system generally
org.anchoranalysis.core.system.path - package org.anchoranalysis.core.system.path
Utilities for converting/manipulating file-paths.
org.anchoranalysis.core.value - package org.anchoranalysis.core.value
Encapsulating values or sets of named-values.
org.anchoranalysis.experiment - package org.anchoranalysis.experiment
Classes related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean - package org.anchoranalysis.experiment.bean
Beans related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean.identifier - package org.anchoranalysis.experiment.bean.identifier
Assigning unique names to experiments.
org.anchoranalysis.experiment.bean.io - package org.anchoranalysis.experiment.bean.io
Generic experiments that handle input and output in structured ways.
org.anchoranalysis.experiment.bean.log - package org.anchoranalysis.experiment.bean.log
Different approaches to where messages on the progress/status of an experiment are logged to.
org.anchoranalysis.experiment.bean.processor - package org.anchoranalysis.experiment.bean.processor
How a task is executed on multiple inputs.
org.anchoranalysis.experiment.bean.require - package org.anchoranalysis.experiment.bean.require
A test whether certain conditions on arguments to experiments are fulfilled.
org.anchoranalysis.experiment.bean.task - package org.anchoranalysis.experiment.bean.task
Defines a task, which is a set of operations run on an input, that may or may not generate an output.
org.anchoranalysis.experiment.io - package org.anchoranalysis.experiment.io
Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.log - package org.anchoranalysis.experiment.log
Helpful classes for logging.
org.anchoranalysis.experiment.task - package org.anchoranalysis.experiment.task
Non-bean classes related to a Task.
org.anchoranalysis.experiment.task.processor - package org.anchoranalysis.experiment.task.processor
Non-bean classes related to JobProcessor.
org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean
Beans pertaining to feature-calculation.
org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list
A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator
Features that are sufficiently generic to work on any input-type.
org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider
Provider of a single feature.
org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results
Defines base class FeatureResults together with some implementations.
org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate
Sub-feature units of calculation that can be cached.
org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache
Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy
 
org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input
 
org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv
Writing feature calculation-results in CSV format.
org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name
Naming items in a weay that breaks down into multiple elements.
org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results
Writes feature-calculation results in different formats, also grouped results.
org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group
Various different outputs that can be written for the a grouped version of the results in ResultsWriter.
org.anchoranalysis.feature.list - package org.anchoranalysis.feature.list
 
org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name
 
org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results
Results from one or more feature calculations.
org.anchoranalysis.feature.session - package org.anchoranalysis.feature.session
 
org.anchoranalysis.feature.session.cache - package org.anchoranalysis.feature.session.cache
 
org.anchoranalysis.feature.session.cache.creator - package org.anchoranalysis.feature.session.cache.creator
 
org.anchoranalysis.feature.session.cache.horizontal - package org.anchoranalysis.feature.session.cache.horizontal
 
org.anchoranalysis.feature.session.calculator - package org.anchoranalysis.feature.session.calculator
 
org.anchoranalysis.feature.session.calculator.cached - package org.anchoranalysis.feature.session.calculator.cached
 
org.anchoranalysis.feature.session.strategy.child - package org.anchoranalysis.feature.session.strategy.child
 
org.anchoranalysis.feature.session.strategy.replace - package org.anchoranalysis.feature.session.strategy.replace
 
org.anchoranalysis.feature.session.strategy.replace.bind - package org.anchoranalysis.feature.session.strategy.replace.bind
 
org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared
Features shared for referencing among calculations.
org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean
Core (bean) classes for image processing.
org.anchoranalysis.image.bean.channel.converter - package org.anchoranalysis.image.bean.channel.converter
Base classes for comparing a channel to another type.
org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator
Beans for specifying image interpolators.
org.anchoranalysis.image.bean.nonbean.error - package org.anchoranalysis.image.bean.nonbean.error
Specific exception types that can be thrown in this module.
org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init
Initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment
Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange
Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object
Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider
Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack
A provider of Stacks.
org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment
Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary
Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object
Base classes to segment a channel into objects.
org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial
Beans to define entities or operate that consider Euclidian space.
org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange
Beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction
Beans to specify a direction.
org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold
Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation
Reusable relations to a threshold.
org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance
Converting quantities of distance between units.
org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent
Converting quantities of extent (area or volume) between units.
org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area
Converting quantities of area between units.
org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume
Converting quantities of volume between units.
org.anchoranalysis.image.core.channel - package org.anchoranalysis.image.core.channel
The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.channel.convert - package org.anchoranalysis.image.core.channel.convert
Converts a channel to other data-types.
org.anchoranalysis.image.core.channel.convert.attached - package org.anchoranalysis.image.core.channel.convert.attached
Converts a channel to another data-type based upon another object to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.channel - package org.anchoranalysis.image.core.channel.convert.attached.channel
Converts a channel to another data-type based upon a Channel to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.histogram - package org.anchoranalysis.image.core.channel.convert.attached.histogram
Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.channel.factory - package org.anchoranalysis.image.core.channel.factory
Factory classes for creating Channel for various voxel data-types.
org.anchoranalysis.image.core.dimensions - package org.anchoranalysis.image.core.dimensions
Classes to describe the size of images or components of images both in voxels and physically.
org.anchoranalysis.image.core.mask - package org.anchoranalysis.image.core.mask
An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine - package org.anchoranalysis.image.core.mask.combine
Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.core.merge - package org.anchoranalysis.image.core.merge
Merges two or more entities.
org.anchoranalysis.image.core.object - package org.anchoranalysis.image.core.object
The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.factory - package org.anchoranalysis.image.core.object.factory
Utilities to create ObjectMask and ObjectCollection.
org.anchoranalysis.image.core.object.label - package org.anchoranalysis.image.core.object.label
Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.object.properties - package org.anchoranalysis.image.core.object.properties
 
org.anchoranalysis.image.core.object.scale - package org.anchoranalysis.image.core.object.scale
Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.object.seed - package org.anchoranalysis.image.core.object.seed
 
org.anchoranalysis.image.core.orientation - package org.anchoranalysis.image.core.orientation
Various methods to specify the orientation (general direction) of an entity.
org.anchoranalysis.image.core.outline - package org.anchoranalysis.image.core.outline
Finds outline voxels i.e.
org.anchoranalysis.image.core.outline.traverser - package org.anchoranalysis.image.core.outline.traverser
Performs a walk on every voxel on the outline of an object-mask.
org.anchoranalysis.image.core.outline.traverser.path - package org.anchoranalysis.image.core.outline.traverser.path
 
org.anchoranalysis.image.core.outline.traverser.visited - package org.anchoranalysis.image.core.outline.traverser.visited
 
org.anchoranalysis.image.core.outline.traverser.visited.combine - package org.anchoranalysis.image.core.outline.traverser.visited.combine
 
org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy - package org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy
 
org.anchoranalysis.image.core.points - package org.anchoranalysis.image.core.points
 
org.anchoranalysis.image.core.stack - package org.anchoranalysis.image.core.stack
 
org.anchoranalysis.image.core.stack.bufferedimage - package org.anchoranalysis.image.core.stack.bufferedimage
 
org.anchoranalysis.image.core.stack.rgb - package org.anchoranalysis.image.core.stack.rgb
 
org.anchoranalysis.image.core.stack.wrap - package org.anchoranalysis.image.core.stack.wrap
 
org.anchoranalysis.image.experiment.bean.task - package org.anchoranalysis.image.experiment.bean.task
 
org.anchoranalysis.image.experiment.identifiers - package org.anchoranalysis.image.experiment.identifiers
 
org.anchoranalysis.image.experiment.label - package org.anchoranalysis.image.experiment.label
 
org.anchoranalysis.image.experiment.seed - package org.anchoranalysis.image.experiment.seed
 
org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean
Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection
 
org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair
 
org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single
 
org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical
 
org.anchoranalysis.image.feature.bean.physical.convert - package org.anchoranalysis.image.feature.bean.physical.convert
 
org.anchoranalysis.image.feature.bean.score - package org.anchoranalysis.image.feature.bean.score
 
org.anchoranalysis.image.feature.bean.stack - package org.anchoranalysis.image.feature.bean.stack
 
org.anchoranalysis.image.feature.evaluator - package org.anchoranalysis.image.feature.evaluator
 
org.anchoranalysis.image.feature.histogram - package org.anchoranalysis.image.feature.histogram
 
org.anchoranalysis.image.feature.object.calculation - package org.anchoranalysis.image.feature.object.calculation
 
org.anchoranalysis.image.feature.object.input - package org.anchoranalysis.image.feature.object.input
 
org.anchoranalysis.image.feature.session - package org.anchoranalysis.image.feature.session
 
org.anchoranalysis.image.feature.session.merged - package org.anchoranalysis.image.feature.session.merged
 
org.anchoranalysis.image.feature.stack - package org.anchoranalysis.image.feature.stack
 
org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel
Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic
Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner
 
org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary
The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values
Defining on and off intensity-values to interpret an image in a binary way.
org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer
 
org.anchoranalysis.image.voxel.buffer.max - package org.anchoranalysis.image.voxel.buffer.max
 
org.anchoranalysis.image.voxel.buffer.mean - package org.anchoranalysis.image.voxel.buffer.mean
 
org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive
Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert
Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2
Converts anchor data-structures to those used by ImgLib2.
org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype
 
org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter
 
org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate
 
org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory
 
org.anchoranalysis.image.voxel.factory.sliceindex - package org.anchoranalysis.image.voxel.factory.sliceindex
 
org.anchoranalysis.image.voxel.interpolator - package org.anchoranalysis.image.voxel.interpolator
Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator
Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting
Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor
Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate
Functional-interfaces for processing different combinations of points and buffers that return a boolean.
org.anchoranalysis.image.voxel.iterator.predicate.buffer - package org.anchoranalysis.image.voxel.iterator.predicate.buffer
 
org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process
Functional-interfaces for processing different combinations of points and buffers that do not return a value.
org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer
Functional-interfaces for processing different combinations of points and raw buffers, but not VoxelBuffer.
org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
Functional-interfaces for processing different combinations of points and VoxelBuffer but not raw buffers.
org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel
 
org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count
 
org.anchoranalysis.image.voxel.kernel.density - package org.anchoranalysis.image.voxel.kernel.density
 
org.anchoranalysis.image.voxel.kernel.dilateerode - package org.anchoranalysis.image.voxel.kernel.dilateerode
 
org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline
 
org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood
 
org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object
 
org.anchoranalysis.image.voxel.object.factory - package org.anchoranalysis.image.voxel.object.factory
 
org.anchoranalysis.image.voxel.object.factory.unionfind - package org.anchoranalysis.image.voxel.object.factory.unionfind
Implements a union-find data-structure for connected-components.
org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological
 
org.anchoranalysis.image.voxel.object.morphological.accept - package org.anchoranalysis.image.voxel.object.morphological.accept
 
org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics
Statistics about voxel intensities.
org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder
Thresholding operations on voxels.
org.anchoranalysis.io.bioformats - package org.anchoranalysis.io.bioformats
Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean - package org.anchoranalysis.io.bioformats.bean
Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean.options - package org.anchoranalysis.io.bioformats.bean.options
User-specified options that can modify an opened-raster (e.g.
org.anchoranalysis.io.bioformats.copyconvert - package org.anchoranalysis.io.bioformats.copyconvert
Converts the byte stream opened by Bioformats into channels of particular data-type.
org.anchoranalysis.io.bioformats.copyconvert.tobyte - package org.anchoranalysis.io.bioformats.copyconvert.tobyte
Converts the byte stream opened by Bioformats into channels of ByteBuffer.
org.anchoranalysis.io.bioformats.copyconvert.tofloat - package org.anchoranalysis.io.bioformats.copyconvert.tofloat
Converts the byte stream opened by Bioformats into channels of FloatBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toint - package org.anchoranalysis.io.bioformats.copyconvert.toint
Converts the byte stream opened by Bioformats into channels of IntBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toshort - package org.anchoranalysis.io.bioformats.copyconvert.toshort
Converts the byte stream opened by Bioformats into channels of ShortBuffer.
org.anchoranalysis.io.generator - package org.anchoranalysis.io.generator
Base-classes and utilities for generators, which write different types of objects to the file system.
org.anchoranalysis.io.generator.collection - package org.anchoranalysis.io.generator.collection
Outputting more than one element collectively using a generator.
org.anchoranalysis.io.generator.combined - package org.anchoranalysis.io.generator.combined
Combining multiple generators into one.
org.anchoranalysis.io.generator.sequence - package org.anchoranalysis.io.generator.sequence
Writing a sequence of elements using a generator.
org.anchoranalysis.io.generator.sequence.pattern - package org.anchoranalysis.io.generator.sequence.pattern
 
org.anchoranalysis.io.generator.serialized - package org.anchoranalysis.io.generator.serialized
Generators for writing serialized objects.
org.anchoranalysis.io.generator.tabular - package org.anchoranalysis.io.generator.tabular
Generators for writing tabular data, including CSV.
org.anchoranalysis.io.generator.text - package org.anchoranalysis.io.generator.text
Generators for writing textual data, including strings.
org.anchoranalysis.io.generator.xml - package org.anchoranalysis.io.generator.xml
Generators for writing XML data.
org.anchoranalysis.io.imagej.bean.stack.writer - package org.anchoranalysis.io.imagej.bean.stack.writer
Raster-writers that use ImageJ to write images to the filesystem.
org.anchoranalysis.io.imagej.convert - package org.anchoranalysis.io.imagej.convert
Converts to and from ImageJ data-structures for images.
org.anchoranalysis.io.manifest - package org.anchoranalysis.io.manifest
 
org.anchoranalysis.io.manifest.deserializer - package org.anchoranalysis.io.manifest.deserializer
Classes to read manifests from the file-system.
org.anchoranalysis.io.manifest.directory - package org.anchoranalysis.io.manifest.directory
Entities to indicate a directory in the manifest.
org.anchoranalysis.io.manifest.directory.sequenced - package org.anchoranalysis.io.manifest.directory.sequenced
Classes related to a directory that has a particular sequence of outputted filenames.
org.anchoranalysis.io.manifest.file - package org.anchoranalysis.io.manifest.file
Entities to indicate a file and its role in the manifest.
org.anchoranalysis.io.manifest.finder - package org.anchoranalysis.io.manifest.finder
Methods to search through a manifest-file to find outputs matching certain conditions.
org.anchoranalysis.io.manifest.finder.match - package org.anchoranalysis.io.manifest.finder.match
Predicates that are useful for matching against particular type of objects in finders.
org.anchoranalysis.io.manifest.operationrecorder - package org.anchoranalysis.io.manifest.operationrecorder
Makes a record of each file/subdirectory written as output.
org.anchoranalysis.io.manifest.sequencetype - package org.anchoranalysis.io.manifest.sequencetype
Predictable patterns of indexes as used in sets of outputted files.
org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean
Beans for the framework around writing files to the file-system.
org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled
Beans indicating whether a particular output is enabled or not.
org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer
Beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled
Non-beans pertaining to whether a particular output is enabled or not.
org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi
Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single
Non-beans that pertain to whether a single level has outputs that are enabled or not.
org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error
Exceptions that may be thrown when writing files to the file-system.
org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle
Methods of naming a file with an index in the file-name.
org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter
Classes for outputting to particular directories.
org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory
BoundDirectory and related classes.
org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer
Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded
Classes for recording the output-names used as they are written / queried.
org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer
Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml
Outputting XML to the file-system.
org.anchoranalysis.launcher - package org.anchoranalysis.launcher
 
org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config
 
org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor
 
org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam
 
org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment
 
org.anchoranalysis.launcher.executor.selectparam.io - package org.anchoranalysis.launcher.executor.selectparam.io
 
org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path
 
org.anchoranalysis.launcher.executor.selectparam.task - package org.anchoranalysis.launcher.executor.selectparam.task
 
org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options
A centralized location for all command-line options used by the launcher.
org.anchoranalysis.launcher.options.outputs - package org.anchoranalysis.launcher.options.outputs
Adding/removing/changing the output(s) from the experiment via command-line-options.
org.anchoranalysis.launcher.parser - package org.anchoranalysis.launcher.parser
 
org.anchoranalysis.math.arithmetic - package org.anchoranalysis.math.arithmetic
Performing primitive type conversion, counting and summing.
org.anchoranalysis.math.equation - package org.anchoranalysis.math.equation
 
org.anchoranalysis.math.histogram - package org.anchoranalysis.math.histogram
The Histogram core data class and related operations.
org.anchoranalysis.math.moment - package org.anchoranalysis.math.moment
 
org.anchoranalysis.math.optimization - package org.anchoranalysis.math.optimization
 
org.anchoranalysis.math.relation - package org.anchoranalysis.math.relation
Different kinds of binary-relations.
org.anchoranalysis.math.statistics - package org.anchoranalysis.math.statistics
 
org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean
 
org.anchoranalysis.mpp.bean.anneal - package org.anchoranalysis.mpp.bean.anneal
 
org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound
 
org.anchoranalysis.mpp.bean.init - package org.anchoranalysis.mpp.bean.init
 
org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark
 
org.anchoranalysis.mpp.bean.mark.bounds - package org.anchoranalysis.mpp.bean.mark.bounds
 
org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory
 
org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points
 
org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter
 
org.anchoranalysis.mpp.bean.points.updatable - package org.anchoranalysis.mpp.bean.points.updatable
 
org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer
 
org.anchoranalysis.mpp.bean.proposer.radii - package org.anchoranalysis.mpp.bean.proposer.radii
 
org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider
 
org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap
 
org.anchoranalysis.mpp.bound - package org.anchoranalysis.mpp.bound
 
org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria
 
org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element
 
org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme
 
org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark
 
org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection
 
org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy
 
org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks
 
org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved
 
org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme
 
org.anchoranalysis.mpp.feature.error - package org.anchoranalysis.mpp.feature.error
 
org.anchoranalysis.mpp.feature.input.memo - package org.anchoranalysis.mpp.feature.input.memo
 
org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark
 
org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input
 
org.anchoranalysis.mpp.io.bean.report.feature - package org.anchoranalysis.mpp.io.bean.report.feature
 
org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input
 
org.anchoranalysis.mpp.io.marks - package org.anchoranalysis.mpp.io.marks
 
org.anchoranalysis.mpp.io.marks.generator - package org.anchoranalysis.mpp.io.marks.generator
 
org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output
 
org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark
 
org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic
 
org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points
 
org.anchoranalysis.mpp.mark.set - package org.anchoranalysis.mpp.mark.set
 
org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized
 
org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo
 
org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap
 
org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay
 
org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair
 
org.anchoranalysis.mpp.points - package org.anchoranalysis.mpp.points
 
org.anchoranalysis.mpp.probmap - package org.anchoranalysis.mpp.probmap
 
org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer
 
org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error
 
org.anchoranalysis.mpp.proposer.visualization - package org.anchoranalysis.mpp.proposer.visualization
 
org.anchoranalysis.mpp.segment.bean - package org.anchoranalysis.mpp.segment.bean
Beans for segmentation algorithms related to marked-point-processes.
org.anchoranalysis.mpp.segment.bean.define - package org.anchoranalysis.mpp.segment.bean.define
DefineOutputter and its sub-classes.
org.anchoranalysis.mpp.segment.bean.kernel - package org.anchoranalysis.mpp.segment.bean.kernel
Base classes for kernels that transition a configuration of marks (a MarkCollection) into an altered version.
org.anchoranalysis.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.mpp.segment.bean.kernel.proposer
 
org.anchoranalysis.mpp.segment.bean.optimization - package org.anchoranalysis.mpp.segment.bean.optimization
 
org.anchoranalysis.mpp.segment.bean.optimization.feedback - package org.anchoranalysis.mpp.segment.bean.optimization.feedback
 
org.anchoranalysis.mpp.segment.bean.optimization.termination - package org.anchoranalysis.mpp.segment.bean.optimization.termination
 
org.anchoranalysis.mpp.segment.define - package org.anchoranalysis.mpp.segment.define
 
org.anchoranalysis.mpp.segment.kernel - package org.anchoranalysis.mpp.segment.kernel
 
org.anchoranalysis.mpp.segment.kernel.proposer - package org.anchoranalysis.mpp.segment.kernel.proposer
 
org.anchoranalysis.mpp.segment.optimization - package org.anchoranalysis.mpp.segment.optimization
 
org.anchoranalysis.mpp.segment.optimization.feedback - package org.anchoranalysis.mpp.segment.optimization.feedback
 
org.anchoranalysis.mpp.segment.optimization.feedback.aggregate - package org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
 
org.anchoranalysis.mpp.segment.optimization.feedback.period - package org.anchoranalysis.mpp.segment.optimization.feedback.period
 
org.anchoranalysis.mpp.segment.optimization.step - package org.anchoranalysis.mpp.segment.optimization.step
 
org.anchoranalysis.mpp.segment.transformer - package org.anchoranalysis.mpp.segment.transformer
 
org.anchoranalysis.mpp.voxel.partition - package org.anchoranalysis.mpp.voxel.partition
 
org.anchoranalysis.mpp.voxel.partition.factory - package org.anchoranalysis.mpp.voxel.partition.factory
 
org.anchoranalysis.overlay - package org.anchoranalysis.overlay
 
org.anchoranalysis.overlay.bean - package org.anchoranalysis.overlay.bean
 
org.anchoranalysis.overlay.collection - package org.anchoranalysis.overlay.collection
 
org.anchoranalysis.overlay.identifier - package org.anchoranalysis.overlay.identifier
 
org.anchoranalysis.overlay.object - package org.anchoranalysis.overlay.object
 
org.anchoranalysis.overlay.object.scaled - package org.anchoranalysis.overlay.object.scaled
 
org.anchoranalysis.overlay.writer - package org.anchoranalysis.overlay.writer
 
org.anchoranalysis.plot - package org.anchoranalysis.plot
Plotting data on charts.
org.anchoranalysis.plot.bean - package org.anchoranalysis.plot.bean
Beans for plotting.
org.anchoranalysis.plot.bean.colorscheme - package org.anchoranalysis.plot.bean.colorscheme
Color schemes associated with plots.
org.anchoranalysis.plot.index - package org.anchoranalysis.plot.index
Non-bean plot definitions.
org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate
Beans to combine two or more annotations.
org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer
Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.bean.comparison - package org.anchoranalysis.plugin.annotation.bean.comparison
 
org.anchoranalysis.plugin.annotation.bean.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner
Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file
FilesProviders for providing annotations.
org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label
A label as used for annotating.
org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy
Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison
Non-bean classes for comparing two sets of annotations.
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
Morphological grayscale-reconstruction algorithm.
org.anchoranalysis.plugin.fiji.bean.channel.provider - package org.anchoranalysis.plugin.fiji.bean.channel.provider
Implementations of ChannelProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.define - package org.anchoranalysis.plugin.fiji.bean.define
Implementations of DefineAdderBean that use FIJI.
org.anchoranalysis.plugin.fiji.bean.mask.provider - package org.anchoranalysis.plugin.fiji.bean.mask.provider
Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.threshold - package org.anchoranalysis.plugin.fiji.bean.threshold
Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur
 
org.anchoranalysis.plugin.image.bean.box - package org.anchoranalysis.plugin.image.bean.box
Beans pertaining to bounding-boxes.
org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert
 
org.anchoranalysis.plugin.image.bean.channel.convert.histogram - package org.anchoranalysis.plugin.image.bean.channel.convert.histogram
 
org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider
 
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign
 
org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert
 
org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient
 
org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity
 
org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask
 
org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object
 
org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score
 
org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice
 
org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider
 
org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider
 
org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider
 
org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold
 
org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider
 
org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine
 
org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert
 
org.anchoranalysis.plugin.image.bean.mask.provider.dimensions - package org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
 
org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological
 
org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate
 
org.anchoranalysis.plugin.image.bean.mask.provider.resize - package org.anchoranalysis.plugin.image.bean.mask.provider.resize
 
org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment
 
org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice
 
org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter
 
org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine
 
org.anchoranalysis.plugin.image.bean.object.filter.dependent - package org.anchoranalysis.plugin.image.bean.object.filter.dependent
 
org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent
 
org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match
 
org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider
 
org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected
 
org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature
 
org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter
 
org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask
 
org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge
 
org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological
 
org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment
 
org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice
 
org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split
 
org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel
 
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
 
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
 
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
 
org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce
Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.object.segment.stack - package org.anchoranalysis.plugin.image.bean.object.segment.stack
Instance-segmentation of a Stack.
org.anchoranalysis.plugin.image.bean.params - package org.anchoranalysis.plugin.image.bean.params
 
org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale
 
org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary
 
org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider
 
org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color
 
org.anchoranalysis.plugin.image.bean.stack.provider.plot - package org.anchoranalysis.plugin.image.bean.stack.provider.plot
 
org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object
 
org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack
 
org.anchoranalysis.plugin.image.box - package org.anchoranalysis.plugin.image.box
Non-beans pertaining to bounding-boxes.
org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel
 
org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions
 
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
 
org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair
 
org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute
 
org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological
 
org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection
 
org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine
 
org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair
 
org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap - package org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
 
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching - package org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
 
org.anchoranalysis.plugin.image.feature.bean.object.single - package org.anchoranalysis.plugin.image.feature.bean.object.single
 
org.anchoranalysis.plugin.image.feature.bean.object.single.border - package org.anchoranalysis.plugin.image.feature.bean.object.single.border
 
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox - package org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
 
org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy
 
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
 
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
 
org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments
 
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
 
org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape
 
org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared
 
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
 
org.anchoranalysis.plugin.image.feature.bean.object.single.slice - package org.anchoranalysis.plugin.image.feature.bean.object.single.slice
 
org.anchoranalysis.plugin.image.feature.bean.object.single.surface - package org.anchoranalysis.plugin.image.feature.bean.object.single.surface
 
org.anchoranalysis.plugin.image.feature.bean.physical - package org.anchoranalysis.plugin.image.feature.bean.physical
 
org.anchoranalysis.plugin.image.feature.bean.score - package org.anchoranalysis.plugin.image.feature.bean.score
 
org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared
 
org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object
 
org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity
 
org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object
 
org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object
 
org.anchoranalysis.plugin.image.feature.object.calculation.delegate - package org.anchoranalysis.plugin.image.feature.object.calculation.delegate
 
org.anchoranalysis.plugin.image.feature.object.calculation.single - package org.anchoranalysis.plugin.image.feature.object.calculation.single
 
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
 
org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation
 
org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity
 
org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level
 
org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object
 
org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge
 
org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition
 
org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority
 
org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider
 
org.anchoranalysis.plugin.image.segment - package org.anchoranalysis.plugin.image.segment
 
org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice
 
org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding
 
org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature
Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source - package org.anchoranalysis.plugin.image.task.bean.feature.source
Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.image.task.bean.format - package org.anchoranalysis.plugin.image.task.bean.format
Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package org.anchoranalysis.plugin.image.task.bean.format.convertstyle
Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
org.anchoranalysis.plugin.image.task.bean.grouped - package org.anchoranalysis.plugin.image.task.bean.grouped
Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram
Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.bean.grouped.raster - package org.anchoranalysis.plugin.image.task.bean.grouped.raster
Task(s) to calculate the mean of channels grouped together.
org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
Selecting a subset of a set of channels.
org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller
Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale
 
org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment
Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice - package org.anchoranalysis.plugin.image.task.bean.slice
Tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.image.task.channel - package org.anchoranalysis.plugin.image.task.channel
Non-bean classes pertaining to Channels as used in tasks.
org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature
Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator
Non-beans for calculating Features.
org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped
Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller
Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment
Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.slice - package org.anchoranalysis.plugin.image.task.slice
Non-bean cleasses pertaining to tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail
Non-bean classes for thumbnail creation.
org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider
 
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
 
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
 
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
 
org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define
 
org.anchoranalysis.plugin.imagej.bean.interpolator - package org.anchoranalysis.plugin.imagej.bean.interpolator
 
org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider
 
org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider
 
org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment
 
org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider
 
org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold
 
org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider
 
org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask
 
org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map
 
org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod - package org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
 
org.anchoranalysis.plugin.io.bean.copyfilesmode.naming - package org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
 
org.anchoranalysis.plugin.io.bean.descriptivename - package org.anchoranalysis.plugin.io.bean.descriptivename
 
org.anchoranalysis.plugin.io.bean.descriptivename.patternspan - package org.anchoranalysis.plugin.io.bean.descriptivename.patternspan
 
org.anchoranalysis.plugin.io.bean.experiment - package org.anchoranalysis.plugin.io.bean.experiment
 
org.anchoranalysis.plugin.io.bean.filepath - package org.anchoranalysis.plugin.io.bean.filepath
 
org.anchoranalysis.plugin.io.bean.filepath.prefixer - package org.anchoranalysis.plugin.io.bean.filepath.prefixer
 
org.anchoranalysis.plugin.io.bean.groupfiles - package org.anchoranalysis.plugin.io.bean.groupfiles
 
org.anchoranalysis.plugin.io.bean.groupfiles.check - package org.anchoranalysis.plugin.io.bean.groupfiles.check
 
org.anchoranalysis.plugin.io.bean.groupfiles.parser - package org.anchoranalysis.plugin.io.bean.groupfiles.parser
 
org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input
 
org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel
 
org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files
 
org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider
 
org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter
 
org.anchoranalysis.plugin.io.bean.input.manifest - package org.anchoranalysis.plugin.io.bean.input.manifest
 
org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack
 
org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive
 
org.anchoranalysis.plugin.io.bean.provider.file - package org.anchoranalysis.plugin.io.bean.provider.file
 
org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader
 
org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer
 
org.anchoranalysis.plugin.io.bean.stack.writer.bioformats - package org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
 
org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer
 
org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image
 
org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input
 
org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path
 
org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task
 
org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter
 
org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path
 
org.anchoranalysis.plugin.io.manifest - package org.anchoranalysis.plugin.io.manifest
 
org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile
 
org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer
 
org.anchoranalysis.plugin.io.summarizer - package org.anchoranalysis.plugin.io.summarizer
 
org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml
Reading and writing metadata XML.
org.anchoranalysis.plugin.ml.bean.classifier - package org.anchoranalysis.plugin.ml.bean.classifier
 
org.anchoranalysis.plugin.ml.bean.cluster - package org.anchoranalysis.plugin.ml.bean.cluster
Beans that perform clustering in some way.
org.anchoranalysis.plugin.mpp.bean.addcriteria - package org.anchoranalysis.plugin.mpp.bean.addcriteria
 
org.anchoranalysis.plugin.mpp.bean.bound - package org.anchoranalysis.plugin.mpp.bean.bound
 
org.anchoranalysis.plugin.mpp.bean.check - package org.anchoranalysis.plugin.mpp.bean.check
 
org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define
 
org.anchoranalysis.plugin.mpp.bean.distance - package org.anchoranalysis.plugin.mpp.bean.distance
 
org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider
 
org.anchoranalysis.plugin.mpp.bean.outline - package org.anchoranalysis.plugin.mpp.bean.outline
 
org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler - package org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
 
org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
 
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
 
org.anchoranalysis.plugin.mpp.bean.proposer.merge - package org.anchoranalysis.plugin.mpp.bean.proposer.merge
 
org.anchoranalysis.plugin.mpp.bean.proposer.orientation - package org.anchoranalysis.plugin.mpp.bean.proposer.orientation
 
org.anchoranalysis.plugin.mpp.bean.proposer.points - package org.anchoranalysis.plugin.mpp.bean.proposer.points
 
org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation - package org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
 
org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline - package org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline
 
org.anchoranalysis.plugin.mpp.bean.proposer.position - package org.anchoranalysis.plugin.mpp.bean.proposer.position
 
org.anchoranalysis.plugin.mpp.bean.proposer.radii - package org.anchoranalysis.plugin.mpp.bean.proposer.radii
 
org.anchoranalysis.plugin.mpp.bean.proposer.scalar - package org.anchoranalysis.plugin.mpp.bean.proposer.scalar
 
org.anchoranalysis.plugin.mpp.bean.proposer.split - package org.anchoranalysis.plugin.mpp.bean.proposer.split
 
org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection
 
org.anchoranalysis.plugin.mpp.bean.provider.single - package org.anchoranalysis.plugin.mpp.bean.provider.single
 
org.anchoranalysis.plugin.mpp.bean.region - package org.anchoranalysis.plugin.mpp.bean.region
 
org.anchoranalysis.plugin.mpp.bean.segment.binary - package org.anchoranalysis.plugin.mpp.bean.segment.binary
 
org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider
 
org.anchoranalysis.plugin.mpp.experiment.bean - package org.anchoranalysis.plugin.mpp.experiment.bean
 
org.anchoranalysis.plugin.mpp.experiment.bean.define - package org.anchoranalysis.plugin.mpp.experiment.bean.define
 
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
 
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
 
org.anchoranalysis.plugin.mpp.experiment.bean.feature.source - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
 
org.anchoranalysis.plugin.mpp.experiment.bean.objects - package org.anchoranalysis.plugin.mpp.experiment.bean.objects
 
org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition - package org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
 
org.anchoranalysis.plugin.mpp.experiment.bean.output - package org.anchoranalysis.plugin.mpp.experiment.bean.output
 
org.anchoranalysis.plugin.mpp.experiment.bean.segment - package org.anchoranalysis.plugin.mpp.experiment.bean.segment
 
org.anchoranalysis.plugin.mpp.experiment.objects - package org.anchoranalysis.plugin.mpp.experiment.objects
 
org.anchoranalysis.plugin.mpp.experiment.objects.csv - package org.anchoranalysis.plugin.mpp.experiment.objects.csv
 
org.anchoranalysis.plugin.mpp.feature.bean.mark.collection - package org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
 
org.anchoranalysis.plugin.mpp.feature.bean.mark.direction - package org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
 
org.anchoranalysis.plugin.mpp.feature.bean.mark.radii - package org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
 
org.anchoranalysis.plugin.mpp.feature.bean.mark.region - package org.anchoranalysis.plugin.mpp.feature.bean.mark.region
 
org.anchoranalysis.plugin.mpp.feature.bean.memo.all - package org.anchoranalysis.plugin.mpp.feature.bean.memo.all
 
org.anchoranalysis.plugin.mpp.feature.bean.memo.ind - package org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
 
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
 
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
 
org.anchoranalysis.plugin.mpp.feature.bean.unit - package org.anchoranalysis.plugin.mpp.feature.bean.unit
 
org.anchoranalysis.plugin.mpp.feature.overlap - package org.anchoranalysis.plugin.mpp.feature.overlap
 
org.anchoranalysis.plugin.mpp.segment - package org.anchoranalysis.plugin.mpp.segment
 
org.anchoranalysis.plugin.mpp.segment.bean.annealing - package org.anchoranalysis.plugin.mpp.segment.bean.annealing
 
org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
 
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
 
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
 
org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
 
org.anchoranalysis.plugin.mpp.segment.bean.marks - package org.anchoranalysis.plugin.mpp.segment.bean.marks
 
org.anchoranalysis.plugin.mpp.segment.bean.marks.dual - package org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
 
org.anchoranalysis.plugin.mpp.segment.bean.marks.partition - package org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
 
org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
 
org.anchoranalysis.plugin.mpp.segment.bean.marks.weight - package org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
 
org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
 
org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
 
org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
 
org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
 
org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
 
org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
 
org.anchoranalysis.plugin.mpp.segment.kernel.assigner - package org.anchoranalysis.plugin.mpp.segment.kernel.assigner
 
org.anchoranalysis.plugin.mpp.segment.kernel.updater - package org.anchoranalysis.plugin.mpp.segment.kernel.updater
 
org.anchoranalysis.plugin.mpp.segment.optimization - package org.anchoranalysis.plugin.mpp.segment.optimization
 
org.anchoranalysis.plugin.opencv - package org.anchoranalysis.plugin.opencv
 
org.anchoranalysis.plugin.opencv.bean.feature - package org.anchoranalysis.plugin.opencv.bean.feature
 
org.anchoranalysis.plugin.opencv.bean.object.segment.stack - package org.anchoranalysis.plugin.opencv.bean.object.segment.stack
 
org.anchoranalysis.plugin.opencv.bean.stack.provider.color - package org.anchoranalysis.plugin.opencv.bean.stack.provider.color
 
org.anchoranalysis.plugin.opencv.bean.writer - package org.anchoranalysis.plugin.opencv.bean.writer
Implementations of StackWriter and any other types of writers that use OpenCV.
org.anchoranalysis.plugin.opencv.convert - package org.anchoranalysis.plugin.opencv.convert
 
org.anchoranalysis.plugin.operator.feature.bean - package org.anchoranalysis.plugin.operator.feature.bean
 
org.anchoranalysis.plugin.operator.feature.bean.arithmetic - package org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
org.anchoranalysis.plugin.operator.feature.bean.conditional - package org.anchoranalysis.plugin.operator.feature.bean.conditional
 
org.anchoranalysis.plugin.operator.feature.bean.list - package org.anchoranalysis.plugin.operator.feature.bean.list
 
org.anchoranalysis.plugin.operator.feature.bean.range - package org.anchoranalysis.plugin.operator.feature.bean.range
 
org.anchoranalysis.plugin.operator.feature.bean.range.feature - package org.anchoranalysis.plugin.operator.feature.bean.range.feature
 
org.anchoranalysis.plugin.operator.feature.bean.replace - package org.anchoranalysis.plugin.operator.feature.bean.replace
 
org.anchoranalysis.plugin.operator.feature.bean.score - package org.anchoranalysis.plugin.operator.feature.bean.score
 
org.anchoranalysis.plugin.operator.feature.physical - package org.anchoranalysis.plugin.operator.feature.physical
 
org.anchoranalysis.plugin.operator.feature.score - package org.anchoranalysis.plugin.operator.feature.score
 
org.anchoranalysis.plugin.points.bean.contour - package org.anchoranalysis.plugin.points.bean.contour
 
org.anchoranalysis.plugin.points.bean.feature.object.conic - package org.anchoranalysis.plugin.points.bean.feature.object.conic
 
org.anchoranalysis.plugin.points.bean.fitter - package org.anchoranalysis.plugin.points.bean.fitter
 
org.anchoranalysis.plugin.points.bean.mark.proposer.single - package org.anchoranalysis.plugin.points.bean.mark.proposer.single
 
org.anchoranalysis.plugin.points.bean.mark.provider.collection - package org.anchoranalysis.plugin.points.bean.mark.provider.collection
 
org.anchoranalysis.plugin.points.bean.mark.provider.single - package org.anchoranalysis.plugin.points.bean.mark.provider.single
 
org.anchoranalysis.plugin.points.bean.mask.provider - package org.anchoranalysis.plugin.points.bean.mask.provider
 
org.anchoranalysis.plugin.points.bean.provider.object - package org.anchoranalysis.plugin.points.bean.provider.object
 
org.anchoranalysis.plugin.points.calculate - package org.anchoranalysis.plugin.points.calculate
 
org.anchoranalysis.plugin.points.calculate.ellipse - package org.anchoranalysis.plugin.points.calculate.ellipse
 
org.anchoranalysis.plugin.points.calculate.ellipsoid - package org.anchoranalysis.plugin.points.calculate.ellipsoid
 
org.anchoranalysis.plugin.points.contour - package org.anchoranalysis.plugin.points.contour
 
org.anchoranalysis.plugin.points.convexhull - package org.anchoranalysis.plugin.points.convexhull
 
org.anchoranalysis.plugin.quick.bean.experiment - package org.anchoranalysis.plugin.quick.bean.experiment
 
org.anchoranalysis.plugin.quick.bean.file.path.derive - package org.anchoranalysis.plugin.quick.bean.file.path.derive
 
org.anchoranalysis.plugin.quick.bean.input - package org.anchoranalysis.plugin.quick.bean.input
 
org.anchoranalysis.plugin.quick.bean.input.filepathappend - package org.anchoranalysis.plugin.quick.bean.input.filepathappend
 
org.anchoranalysis.plugin.quick.bean.structure - package org.anchoranalysis.plugin.quick.bean.structure
 
org.anchoranalysis.spatial - package org.anchoranalysis.spatial
 
org.anchoranalysis.spatial.axis - package org.anchoranalysis.spatial.axis
Identifying the three standard axes in 3D cartesian coordinates.
org.anchoranalysis.spatial.box - package org.anchoranalysis.spatial.box
Axis-aligned bounding-boxes and related operations.
org.anchoranalysis.spatial.point - package org.anchoranalysis.spatial.point
A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
org.anchoranalysis.spatial.point.consumer - package org.anchoranalysis.spatial.point.consumer
Functional interfaces that accept cartesian coordinate points specified in different ways.
org.anchoranalysis.spatial.rotation - package org.anchoranalysis.spatial.rotation
A matrix to apply a rotation to a point.
org.anchoranalysis.spatial.rotation.factory - package org.anchoranalysis.spatial.rotation.factory
Creates RotationMatrix in varying ways.
org.anchoranalysis.spatial.rtree - package org.anchoranalysis.spatial.rtree
R-Tree data structure and related operations.
org.anchoranalysis.spatial.scale - package org.anchoranalysis.spatial.scale
How to much to scale an entity in Cartesian space by.
org.anchoranalysis.test - package org.anchoranalysis.test
Testing utilities and fixtures with no greater downstream dependency than anchor-core.
org.anchoranalysis.test.experiment - package org.anchoranalysis.test.experiment
Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
org.anchoranalysis.test.experiment.launcher - package org.anchoranalysis.test.experiment.launcher
Launches an anchor binary from a shell and runs an experiment.
org.anchoranalysis.test.feature - package org.anchoranalysis.test.feature
Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
org.anchoranalysis.test.feature.plugins - package org.anchoranalysis.test.feature.plugins
Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.
org.anchoranalysis.test.feature.plugins.mockfeature - package org.anchoranalysis.test.feature.plugins.mockfeature
A mocked feature internally using a feature-calculation.
org.anchoranalysis.test.feature.plugins.objects - package org.anchoranalysis.test.feature.plugins.objects
Fixtures for creating object-masks and related feature-inputs.
OrientableBounds - Class in org.anchoranalysis.mpp.bean.bound
 
OrientableBounds() - Constructor for class org.anchoranalysis.mpp.bean.bound.OrientableBounds
 
Orientation - Class in org.anchoranalysis.image.core.orientation
 
Orientation() - Constructor for class org.anchoranalysis.image.core.orientation.Orientation
 
Orientation2D - Class in org.anchoranalysis.image.core.orientation
 
Orientation2D() - Constructor for class org.anchoranalysis.image.core.orientation.Orientation2D
 
Orientation2D(double) - Constructor for class org.anchoranalysis.image.core.orientation.Orientation2D
 
Orientation3DEulerAngles - Class in org.anchoranalysis.image.core.orientation
 
Orientation3DEulerAngles() - Constructor for class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
Orientation3DEulerAngles(double, double, double) - Constructor for class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
OrientationAndRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
Proposes both an orientation and radii for a ConicBase
OrientationAndRadiiProposer(RadiiProposer, OrientationProposer) - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
 
OrientationAxisAngle - Class in org.anchoranalysis.image.core.orientation
An orientation in axis-angle representation.
OrientationAxisAngle(Vector3d, double) - Constructor for class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
OrientationIdentity - Class in org.anchoranalysis.image.core.orientation
 
OrientationIdentity(int) - Constructor for class org.anchoranalysis.image.core.orientation.OrientationIdentity
 
OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer
 
OrientationProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.OrientationProposer
 
OrientationRotationMatrix - Class in org.anchoranalysis.image.core.orientation
 
OrientationRotationMatrix() - Constructor for class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
OrientationRotationMatrix(RotationMatrix) - Constructor for class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
 
otherVertex(V) - Method in class org.anchoranalysis.core.graph.TypedEdge
The other vertex on the edge
Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
Performs auto-thresholding using Otsu's method.
Otsu() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
 
OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
Similar to Otsu, but weighs the variances differently of background and foreground
OtsuWeighted() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
OtsuWeighted(double, double) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
Provides a prefix which can be prepended to all output files.
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
 
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
 
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
 
outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
outFilePrefixAvoidResolve(NamedPath, String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
Provides a prefix which can be prepended to all output files.
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
 
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
Determines the out-file prefix from a path
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
 
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.FromDescriptiveName
 
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
 
outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
 
outgoingEdgesFor(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
All outgoing edges for a given vertex.
outline(Mask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.outline.FindOutline
Creates an outline of depth 1 from a mask
outline(ObjectMask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.outline.FindOutline
Creates outline from an object
Outline - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
Always creates a new mask for the result (no need to duplicate input)
Outline() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
 
outlineGuess3D(Mask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.outline.FindOutline
Finds the outline of a mask, guessing whether to do this in 2D or 3D depending on if the mask has 3-dimensions
OutlineKernel3 - Class in org.anchoranalysis.image.voxel.kernel.outline
 
OutlineKernel3(BinaryValuesByte, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3
 
OutlineKernel3(BinaryValuesByte, OutlineKernelParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3
 
OutlineKernel3Base - Class in org.anchoranalysis.image.voxel.kernel.outline
 
OutlineKernel3Base(BinaryValuesByte, OutlineKernelParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3Base
 
OutlineKernel3NeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline
 
OutlineKernel3NeighborMatchValue(ObjectMask, BinaryVoxels<UnsignedByteBuffer>, OutlineKernelParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3NeighborMatchValue
 
OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
 
OutlineKernelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
 
OutlineKernelParameters - Class in org.anchoranalysis.image.voxel.kernel.outline
 
OutlineKernelParameters(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
 
OutlinePixelsRetriever - Class in org.anchoranalysis.plugin.mpp.bean.outline
 
OutlinePixelsRetriever() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.OutlinePixelsRetriever
 
OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object
Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it centered in a window of a certain size.
OutlinePreserveRelativeSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
 
OutlineTraverser - Class in org.anchoranalysis.image.core.outline.traverser
 
OutlineTraverser(ObjectMask, ConsiderVisit, boolean, boolean) - Constructor for class org.anchoranalysis.image.core.outline.traverser.OutlineTraverser
 
output(String, boolean) - Method in class org.anchoranalysis.io.generator.collection.NamedProviderOutputter
Outputs the entities using a particular output-name.
OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
If not otherwise specified, the output name for a non-aggregated CSV of the results.
OUTPUT_NAME_MANIFEST - Static variable in class org.anchoranalysis.experiment.bean.io.OutputExperiment
 
OUTPUT_NAME_MANIFEST - Static variable in class org.anchoranalysis.experiment.bean.task.Task
 
OUTPUT_RESULTS - Static variable in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
 
OUTPUT_SUMMARY_CSV - Static variable in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
 
OUTPUT_THUMBNAILS - Static variable in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
 
outputAfterAllTasksAreExecuted(Outputter) - Method in interface org.anchoranalysis.mpp.segment.bean.ExperimentState
 
outputAfterAllTasksAreExecuted(Outputter) - Method in class org.anchoranalysis.plugin.mpp.segment.SgmnMPPState
 
outputBeforeAnyTasksAreExecuted(Outputter) - Method in interface org.anchoranalysis.mpp.segment.bean.ExperimentState
 
outputBeforeAnyTasksAreExecuted(Outputter) - Method in class org.anchoranalysis.plugin.mpp.segment.SgmnMPPState
 
OutputDirectoryAlreadyExistsException - Exception in org.anchoranalysis.io.output.error
When an output-directory already exists.
OutputDirectoryAlreadyExistsException(String) - Constructor for exception org.anchoranalysis.io.output.error.OutputDirectoryAlreadyExistsException
 
OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled
Whether a particular output, identified by a textual name, is enabled or not.
OutputEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.OutputEnabled
 
OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded
Additional output-names to enable or disable from an existing set of output-enabled rules.
OutputEnabledDelta() - Constructor for class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
 
OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled
A specific set of first-level outputs are enabled, to which more can be added.
OutputEnabledMutable(String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
Creates with one or more enabled outputs.
OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
Creates with one or more enabled outputs.
OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules
Bean that specifies an implementation of MultiLevelOutputEnabled.
OutputEnabledRules() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules
 
OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules
Base class for an OutputEnabledRules that specifies particular output-names for first and second levels.
OutputEnableRulesSpecify() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
 
OutputEnableRulesSpecify(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
Create with a specific set of first-level output names.
OutputExperiment - Class in org.anchoranalysis.experiment.bean.io
An experiment that uses a OutputManager to specify the outputting of results.
OutputExperiment() - Constructor for class org.anchoranalysis.experiment.bean.io.OutputExperiment
 
OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.io
SelectParam<Path> factory for outputs.
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
 
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
 
outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
 
outputGroupedData(ConsistentChannelChecker, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
Outputs the "grouped" data to the filesystem
outputHeaderToWriter(PrintWriter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
outputHeaderToWriter(PrintWriter, String) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
OutputManager - Class in org.anchoranalysis.io.output.bean
Responsible for making decisions on where output goes and what form it takes.
OutputManager() - Constructor for class org.anchoranalysis.io.output.bean.OutputManager
 
outputName(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
Match a file whose output-name matches a specific value.
outputNames() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
Names for any outputs produced by ResultsWriter.
OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
 
OutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.OutputNameStyle
 
OutputPattern - Class in org.anchoranalysis.io.generator.sequence.pattern
How the output of the sequence looks on the filesystem and in the manifest.
OutputPattern(Optional<String>, IndexableOutputNameStyle, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
 
OutputPatternIntegerSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
A OutputPattern that outputs a file-name with a trailing integer index.
OutputPatternIntegerSuffix(String, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
Creates in a subdirectory, using the outputName as both the subdirectory name and the prefix.
OutputPatternIntegerSuffix(String, boolean, String, int, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
Creates with a full set of flexibility about how the filename appears and whether a subdirectory is used.
OutputPatternIntegerSuffix(String, int, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
Like OutputPatternIntegerSuffix(String, boolean) but with additional options on the manifest-folder description and whether to check outputs against rules.
OutputPatternIntegerSuffix(String, String) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
Creates in a subdirectory, using the output-name as the subdirectory name, and a specific prefix.
OutputPatternIntegerSuffix(String, String, int, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
Like OutputPatternIntegerSuffix(String, String) but with additional options about the number of digits, the manifest-folder description and whether to check outputs against rules.
OutputPatternStringSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
A OutputPattern that outputs a file-name with a trailing string index.
OutputPatternStringSuffix(String, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternStringSuffix
Creates without a prefix.
OutputPatternStringSuffix(String, boolean, String) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternStringSuffix
Creates with a prefix.
outputSelectParam(CommandLine, String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
Can point to either: a path ending in .xml, assumed to BeanXML for an output manager a directory, set as the outputDirectory in the input-context
outputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.Outputter
 
OutputSequence - Interface in org.anchoranalysis.io.generator.sequence
A sequence of elements that are written to the same directory.
OutputSequenceFactory<T> - Class in org.anchoranalysis.io.generator.sequence
Creates and starts a OutputSequence with a particular generator and context.
OutputSequenceFactory(Generator<T>, OutputterChecked) - Constructor for class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
 
OutputSequenceIncrementing<T> - Class in org.anchoranalysis.io.generator.sequence
A sequence of outputs that use the same generator, where each output increments an index by one in the filename.
OutputSequenceIncrementing(BoundOutputter<T>, int) - Constructor for class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
 
OutputSequenceIndexed<T,​S> - Class in org.anchoranalysis.io.generator.sequence
A sequence of outputs that use the same generator with non-incrementing indexes for each output.
outputSharedObjects(MPPInitParams, OutputterChecked) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
 
OutputtedFile - Class in org.anchoranalysis.io.manifest.file
An entry in a Manifest for an outputted file from an experiment.
OutputtedFile(MutableDirectory, String, String, String, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.manifest.file.OutputtedFile
 
OutputtedFile(MutableDirectory, String, String, String, ManifestDescription) - Constructor for class org.anchoranalysis.io.manifest.file.OutputtedFile
 
Outputter - Class in org.anchoranalysis.io.output.outputter
Like OutputterChecked but exceptions are reported in a ErrorReporter.
Outputter(OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.outputter.Outputter
 
OutputterChecked - Class in org.anchoranalysis.io.output.outputter
A particular directory on the filesystem in which outputting can occur.
OutputterDirectories - Class in org.anchoranalysis.mpp.segment.define
Directories into which collections of different types of objects are written to in a define experiment
OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory
The directory and prefix an outputter writes to.
OutputterTarget(DirectoryWithPrefix, boolean) - Constructor for class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
 
outputToWriter(PrintWriter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
outputToWriter(PrintWriter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
OutputWriteFailedException - Exception in org.anchoranalysis.io.output.error
 
OutputWriteFailedException(String) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
 
OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
 
OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
 
OutputWriteFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
 
OutputWriteSettings - Class in org.anchoranalysis.io.output.bean
Settings for how to write output, including default writers.
OutputWriteSettings() - Constructor for class org.anchoranalysis.io.output.bean.OutputWriteSettings
 
outsideAtThreshold - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
 
OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
OutsideRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
 
OverlapCalculator - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
Calculates overlap between object-masks
OverlapMaskBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
 
OverlapMaskBase() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
 
OverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
 
OverlapMIPBase() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
 
OverlapNumVoxels - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
 
OverlapNumVoxels() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxels
 
OverlapNumVoxelsMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
 
OverlapNumVoxelsMask() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxelsMask
 
overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
 
overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
 
overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
 
OverlappingObject<T> - Class in org.anchoranalysis.image.core.object.label
An object-mask that is founded to overlap with another during labelling.
OverlappingObject(T, ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.label.OverlappingObject
 
OverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
 
OverlapRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
 
OverlapRatioMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
 
OverlapRatioMask() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
 
OverlapRelative - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
Expresses the number of intersecting pixels between two objects as a ratio to something else (denominator)
OverlapRelative() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
 
OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
 
OverlapRelativeToFirst() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToFirst
 
OverlapRelativeToMaxVolume - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
Overlap ratio to the maximum number of pixels
OverlapRelativeToMaxVolume() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
 
OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
 
OverlapRelativeToMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
 
OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
 
OverlapRelativeToSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond
 
overlapScoreFor(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
 
overlapScoreFor(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
The Intersection over Union (IoU) score for two bounding-boxes
overlapScoreFor(T, T) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
A score calculating the overlap between two elements.
OverlapUtilities - Class in org.anchoranalysis.mpp.overlap
 
overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities
 
overlapWithGlobalMask(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
 
overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities
Counts the number of overlapping voxels between two VoxelizedMarkMemo
Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange
 
Overlay - Class in org.anchoranalysis.overlay
 
Overlay() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Overlay
 
Overlay() - Constructor for class org.anchoranalysis.overlay.Overlay
 
overlayBufferedImage(BufferedImage, BufferedImage, int, int) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageOverlay
 
OverlayCollection - Class in org.anchoranalysis.overlay.collection
 
OverlayCollection() - Constructor for class org.anchoranalysis.overlay.collection.OverlayCollection
 
OverlayCollection(Stream<Overlay>) - Constructor for class org.anchoranalysis.overlay.collection.OverlayCollection
 
OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay
Two-way factory.
OverlayCollectionObjectFactory - Class in org.anchoranalysis.overlay.collection
Two-way factory.
OverlayMark - Class in org.anchoranalysis.mpp.overlay
 
OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.overlay.OverlayMark
 
OverlayObjectMask - Class in org.anchoranalysis.overlay.object
 
OverlayObjectMask(ObjectMask, int) - Constructor for class org.anchoranalysis.overlay.object.OverlayObjectMask
 
OverlayProperties - Class in org.anchoranalysis.overlay
 
OverlayProperties() - Constructor for class org.anchoranalysis.overlay.OverlayProperties
 

P

Padding - Class in org.anchoranalysis.image.bean.spatial
Padding (whitespace of certain extent) placed around an object in XY direction and in Z direction.
Padding() - Constructor for class org.anchoranalysis.image.bean.spatial.Padding
 
PairedWithMask - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared
Evaluates the object as a pair-feature together with the binary-mask from the shard objects.
PairedWithMask() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
 
PairNeighbors - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine
Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of single-object features and pair features.
PairNeighbors() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
 
PairPxlMarkMemo - Class in org.anchoranalysis.mpp.pair
 
PairPxlMarkMemo(VoxelizedMarkMemo, VoxelizedMarkMemo) - Constructor for class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
 
PairsTableCalculator - Class in org.anchoranalysis.image.feature.session.merged
A feature-session to evaluate pairs of objects.
PairsTableCalculator(MergedPairsFeatures) - Constructor for class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
PairsTableCalculator(MergedPairsFeatures, MergedPairsInclude, boolean) - Constructor for class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
Pairwise - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
 
Pairwise() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
 
ParallelProcessor<T extends InputFromManager,​S> - Class in org.anchoranalysis.experiment.bean.processor
Executes jobs in parallel
ParallelProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
 
Param<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.operator.feature.bean
Extracts a key-value-param as a double
Param() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.Param
 
ParametersAsFeatures<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
Loads a KeyValueParams as features.
ParametersAsFeatures() - Constructor for class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
 
ParametersExperiment - Class in org.anchoranalysis.experiment.task
Parameters for executing a task, when the manifest, log etc.
ParametersExperiment(ExperimentExecutionArguments, String, Optional<Manifest>, OutputterChecked, PathPrefixer, StatefulMessageLogger, boolean) - Constructor for class org.anchoranalysis.experiment.task.ParametersExperiment
 
ParametersUnbound<T,​S> - Class in org.anchoranalysis.experiment.task
 
ParametersUnbound(ParametersExperiment, T, S, boolean) - Constructor for class org.anchoranalysis.experiment.task.ParametersUnbound
 
ParamFromCollection<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.shared
Retrieves a parameter from a collection in shared-objects.
ParamFromCollection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
 
params() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
ParamsBean<T> - Class in org.anchoranalysis.bean.shared.params
 
ParamsBean() - Constructor for class org.anchoranalysis.bean.shared.params.ParamsBean
 
paramsDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
ParamsInitializer<T> - Interface in org.anchoranalysis.bean.initializable.params
 
parseAndRun(String[], LauncherConfig) - Method in class org.anchoranalysis.launcher.parser.ParseArgumentsAndRunExperiment
Parses the arguments to a command-line experiment and runs an experiment
ParseArgumentsAndRunExperiment - Class in org.anchoranalysis.launcher.parser
A general parser for command-line applications with certain attributes.
ParseArgumentsAndRunExperiment(Logger) - Constructor for class org.anchoranalysis.launcher.parser.ParseArgumentsAndRunExperiment
 
ParsedFilePathBag - Class in org.anchoranalysis.plugin.io.multifile
 
ParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
 
PartitionedMarks - Class in org.anchoranalysis.plugin.mpp.segment.optimization
Binary partition of marks into "available" and "accepted"
PartitionedMarks(MarkCollection, ToDoubleFunction<Mark>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
Constructor
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.FilePath
 
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
 
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
 
path(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DirectoryMatch
 
pathCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
 
PathCreator - Interface in org.anchoranalysis.io.output.path.prefixer
Converts file-paths between relative and absolute.
pathCurrentJAR(Class<?>) - Static method in class org.anchoranalysis.launcher.PathCurrentJarUtilities
Determines the path to the current jar directory (or folder with class files) so we can resolve a properties file
PathCurrentJarUtilities - Class in org.anchoranalysis.launcher
 
PathDifference - Class in org.anchoranalysis.core.system.path
Calculates the "difference" between a path and a base
PathDifferenceException - Exception in org.anchoranalysis.core.system.path
 
PathDifferenceException(String) - Constructor for exception org.anchoranalysis.core.system.path.PathDifferenceException
 
PathDifferenceException(String, Exception) - Constructor for exception org.anchoranalysis.core.system.path.PathDifferenceException
 
pathForBinding() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
 
pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
 
pathForBinding() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
pathForBinding() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
 
pathForBinding() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
 
pathForBinding() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
 
pathForBinding() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
 
pathFromArgument(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.ArgumentConverter
Converts the string passed as a command-line argument to a path.
PathFromGenerator - Class in org.anchoranalysis.plugin.annotation.bean.strategy
 
pathOrDirectory(String[], boolean) - Static method in class org.anchoranalysis.launcher.executor.selectparam.io.OutputFactory
If the argument is a path to a directory, then this directory is set as the default.
pathOrDirectoryOrGlobOrExtension(String[]) - Static method in class org.anchoranalysis.launcher.executor.selectparam.io.InputFactory
 
pathOrTaskName(String[], Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.task.TaskFactory
If the argument a name (no extension, no root, no special-chars apart from forward-slashes), then construct an automatic path to the tasks in the configuration directory.
pathOrTaskNameOrDefault(CommandLine, String, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
Can point to either a path to beanXML
PathPrefixer - Class in org.anchoranalysis.io.output.bean.path.prefixer
 
PathPrefixer() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
 
PathPrefixerAvoidResolve - Class in org.anchoranalysis.io.output.bean.path.prefixer
A file-path-resolver that adds additional methods that perform the same function but output a relative-path rather than an absolute path after fully resolving paths
PathPrefixerAvoidResolve() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
 
PathPrefixerAvoidResolve(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
 
PathPrefixerException - Exception in org.anchoranalysis.io.output.path.prefixer
 
PathPrefixerException(String) - Constructor for exception org.anchoranalysis.io.output.path.prefixer.PathPrefixerException
 
PathPrefixerException(Throwable) - Constructor for exception org.anchoranalysis.io.output.path.prefixer.PathPrefixerException
 
PathRegEx - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
Matches a regex against incoming file-paths to form a prefix for output
PathRegEx() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
 
pathRelativeProperties() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
path to a property file that defines a relative-path to the default experiment in bean XML
pathRelativeToBean(AnchorBean<?>, String) - Static method in class org.anchoranalysis.bean.xml.factory.BeanPathUtilities
 
PatternSpan - Class in org.anchoranalysis.plugin.io.bean.descriptivename.patternspan
Finds a pattern in the descriptive name, and uses the region from the first variable to the last-variable as the descriptive-name
PatternSpan() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.patternspan.PatternSpan
 
PayloadCalculator - Interface in org.anchoranalysis.image.feature.evaluator
 
percentAnnotatedImages() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
percentGreaterEqualTo(int) - Method in class org.anchoranalysis.math.histogram.Histogram
 
percentLeftMatched() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
percentRightMatched() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
percentSkippedAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
 
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
 
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
The binary arithmetic operation that combines the voxel-value and the constant-value
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
 
performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
 
periodEnd(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiver
 
periodEnd(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
 
PeriodicSubdirectoryReporter<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
 
PeriodicSubdirectoryReporter() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
 
PeriodReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.period
 
PeriodReceiverException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.period
 
PeriodReceiverException() - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverException
 
PeriodReceiverException(Exception) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverException
 
PeriodReceiverException(String) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverException
 
PeriodReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.period
 
PeriodReceiverList() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
 
periodStart(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiver
 
periodStart(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
 
PeriodTriggerBank<S> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.period
 
PeriodTriggerBank() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
 
permissive() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
A writer that allows all output-names, and records the written output-names
Permissive - Class in org.anchoranalysis.io.output.bean.rules
Allows all output-names to be outputted in both first and second level.
Permissive() - Constructor for class org.anchoranalysis.io.output.bean.rules.Permissive
 
PermissiveExcept - Class in org.anchoranalysis.io.output.bean.rules
All outputs are enabled except particular ones.
PermissiveExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
 
PermissiveExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
Create with first-level output names
PermutationSetter - Interface in org.anchoranalysis.bean.permute.setter
Imposes a permutation on some property of a bean.
PermutationSetterException - Exception in org.anchoranalysis.bean.permute.setter
 
PermutationSetterException(String) - Constructor for exception org.anchoranalysis.bean.permute.setter.PermutationSetterException
 
PermutationSetterList - Class in org.anchoranalysis.bean.permute.setter
Applies several permutation setters to the same object
PermutationSetterList() - Constructor for class org.anchoranalysis.bean.permute.setter.PermutationSetterList
 
PermutationSetterSingle - Class in org.anchoranalysis.bean.permute.setter
Sets a permutation from a list of fields
PermutationSetterSingle() - Constructor for class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
 
PermutationSetterSingle(Field) - Constructor for class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
 
PermutationSetterUtilities - Class in org.anchoranalysis.bean.permute.setter
 
Permute - Class in org.anchoranalysis.plugin.image.bean.object.provider
Permutes some changes over an ObjectCollectionProvider and collects all the results in an ObjectCollection
Permute() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Permute
 
PermuteDivideByParam<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
PermuteDivideByParam() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
 
PermuteFeature<S,​T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
Permutes one or more properties of a Feature, so as to create a set of Features
PermuteFeature() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
 
PermuteFeatureBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
Creates permutations of a feature by modifying a particular property of it in different ways.
PermuteFeatureBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
 
PermuteFeatureSequenceInteger<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
Permutes a property on a feature with a sequence of integers.
PermuteFeatureSequenceInteger() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
PermuteFirstSecondOrder<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
 
PermuteFirstSecondOrder(PermuteFirstSecondOrder.CreateFirstSecondOrder<T>, double, double) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
 
PermuteFirstSecondOrder.CreateFirstSecondOrder<T extends FeatureInput> - Interface in org.anchoranalysis.plugin.image.feature.bean.list.permute
 
PermuteGaussianScore<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
PermuteGaussianScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteGaussianScore
 
PermuteProperty<T> - Class in org.anchoranalysis.bean.permute.property
 
PermuteProperty() - Constructor for class org.anchoranalysis.bean.permute.property.PermuteProperty
 
PermutePropertyDescribeIndex - Class in org.anchoranalysis.bean.permute.property
Proxies an existing PermuteProperty but replaces the existing naming behaviour
PermutePropertyDescribeIndex() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
 
PermutePropertyDoubleSet - Class in org.anchoranalysis.bean.permute.property
 
PermutePropertyDoubleSet() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
 
PermutePropertySequence<T> - Class in org.anchoranalysis.bean.permute.property
Base class for permute-properties involving a sequence of numbers
PermutePropertySequence() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequence
 
PermutePropertySequenceDouble - Class in org.anchoranalysis.bean.permute.property
An arithmetic sequence of doubles, obtained by dividing an integer sequence by a divider
PermutePropertySequenceDouble() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
 
PermutePropertySequenceDouble.DoubleRange - Class in org.anchoranalysis.bean.permute.property
 
PermutePropertySequenceInteger - Class in org.anchoranalysis.bean.permute.property
An arithmetic sequence of doubles, obtained by dividing an integer sequence by a divider
PermutePropertySequenceInteger() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
 
PermutePropertySequenceIntegerWithinString - Class in org.anchoranalysis.bean.permute.property
 
PermutePropertySequenceIntegerWithinString() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
 
PermutePropertyStringSet - Class in org.anchoranalysis.bean.permute.property
 
PermutePropertyStringSet() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
 
PermutePropertyWithPath<T> - Class in org.anchoranalysis.bean.permute.property
Base classes for PermuteProperty that require a path
PermutePropertyWithPath() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
 
PermuteZScore<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
PermuteZScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteZScore
 
Plot<T> - Class in org.anchoranalysis.plot.bean
Defines a plot as a function of data and axis-limits.
Plot() - Constructor for class org.anchoranalysis.plot.bean.Plot
 
PlotAxisLabels - Class in org.anchoranalysis.plot.index
Labels for x and y axis in graph
PlotAxisLabels() - Constructor for class org.anchoranalysis.plot.index.PlotAxisLabels
 
PlotColorScheme - Class in org.anchoranalysis.plot.bean.colorscheme
 
PlotColorScheme() - Constructor for class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
PlotHistogram - Class in org.anchoranalysis.plugin.image.bean.stack.provider.plot
Plots a histogram onto a stack.
PlotHistogram() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
 
PlotIndexBase<T,​S extends org.jfree.data.general.Dataset> - Class in org.anchoranalysis.plot.index
 
PlotIndexBase(String, String[]) - Constructor for class org.anchoranalysis.plot.index.PlotIndexBase
Constructor
PlotIndexBaseCategorical<T,​S extends org.jfree.data.category.CategoryDataset> - Class in org.anchoranalysis.plot.index
Base class for plots involving categorical data types.
PlotIndexBaseCategorical(String, String[], GetForSeries<T, String>, GetForSeries<T, Paint>) - Constructor for class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
 
PlotInstance - Class in org.anchoranalysis.plot
A Plot combined with data and parameters, ready to be displayed.
PlotInstance(JFreeChart, Optional<AxisLimits>) - Constructor for class org.anchoranalysis.plot.PlotInstance
 
pluralize(String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities
Given something, returns somethings
pluralizeMaybe(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities
Returns something or somethings depending on the number
PNG - Class in org.anchoranalysis.io.imagej.bean.stack.writer
Writes a PNG image using ImageJ.
PNG() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
 
point(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
Is this point within the bounding-box?
Point2d - Class in org.anchoranalysis.spatial.point
 
Point2d() - Constructor for class org.anchoranalysis.spatial.point.Point2d
 
Point2d(double, double) - Constructor for class org.anchoranalysis.spatial.point.Point2d
 
Point2d(Point2d) - Constructor for class org.anchoranalysis.spatial.point.Point2d
 
Point2f - Class in org.anchoranalysis.spatial.point
 
Point2f() - Constructor for class org.anchoranalysis.spatial.point.Point2f
 
Point2f(float, float) - Constructor for class org.anchoranalysis.spatial.point.Point2f
 
Point2i - Class in org.anchoranalysis.spatial.point
 
Point2i() - Constructor for class org.anchoranalysis.spatial.point.Point2i
 
Point2i(int, int) - Constructor for class org.anchoranalysis.spatial.point.Point2i
 
Point2i(Point2i) - Constructor for class org.anchoranalysis.spatial.point.Point2i
Copy constructor.
Point3d - Class in org.anchoranalysis.spatial.point
 
Point3d() - Constructor for class org.anchoranalysis.spatial.point.Point3d
 
Point3d(double, double, double) - Constructor for class org.anchoranalysis.spatial.point.Point3d
 
Point3d(Point3f) - Constructor for class org.anchoranalysis.spatial.point.Point3d
 
Point3d(Tuple3d) - Constructor for class org.anchoranalysis.spatial.point.Point3d
 
Point3d(Vector3d) - Constructor for class org.anchoranalysis.spatial.point.Point3d
 
Point3f - Class in org.anchoranalysis.spatial.point
 
Point3f() - Constructor for class org.anchoranalysis.spatial.point.Point3f
 
Point3f(float, float, float) - Constructor for class org.anchoranalysis.spatial.point.Point3f
 
Point3f(Point3f) - Constructor for class org.anchoranalysis.spatial.point.Point3f
 
Point3i - Class in org.anchoranalysis.spatial.point
 
Point3i() - Constructor for class org.anchoranalysis.spatial.point.Point3i
Creates the points with a 0 in each dimension
Point3i(int, int, int) - Constructor for class org.anchoranalysis.spatial.point.Point3i
 
Point3i(ReadableTuple3i) - Constructor for class org.anchoranalysis.spatial.point.Point3i
 
PointClipper - Class in org.anchoranalysis.mpp.points
Ensures a point has values contained inside image-dimensions
PointConverter - Class in org.anchoranalysis.spatial.point
Conversion utilities between different types and dimensionalities of points
pointIgnoreZ(Point3i) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
Is this point within the bounding-box, but ignoring the z-dimension?
PointList - Class in org.anchoranalysis.mpp.mark.points
 
PointList() - Constructor for class org.anchoranalysis.mpp.mark.points.PointList
 
PointList(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointList
 
pointListAtFirstPoint(List<Point3i>) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
Sets all points in a list, to point at the first point (the root point) in the list
PointListBase - Class in org.anchoranalysis.mpp.mark.points
 
PointListBase() - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase
 
PointListBase(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase
 
PointListFactory - Class in org.anchoranalysis.mpp.mark.points
 
pointOnOutline(Point3d, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutline
 
pointOnOutline(Point3d, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
 
PointRange - Class in org.anchoranalysis.spatial.box
Keeps track of the range experienced by points in the x, y and z dimensions
PointRange() - Constructor for class org.anchoranalysis.spatial.box.PointRange
 
points() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
The points associated with the path
points() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
 
PointSampler - Interface in org.anchoranalysis.mpp.probmap
 
PointsBean<T> - Class in org.anchoranalysis.mpp.bean.points
 
PointsBean() - Constructor for class org.anchoranalysis.mpp.bean.points.PointsBean
 
pointsDiscrete() - Method in class org.anchoranalysis.spatial.Contour
 
PointsFitter - Class in org.anchoranalysis.mpp.bean.points.fitter
 
PointsFitter - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks
 
PointsFitter() - Constructor for class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter
 
PointsFitter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
 
PointsFitterException - Exception in org.anchoranalysis.mpp.bean.points.fitter
 
PointsFitterException(Exception) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException
 
PointsFitterException(String) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException
 
PointsFitterFromObjects - Class in org.anchoranalysis.plugin.points.bean.mark.provider.collection
 
PointsFitterFromObjects() - Constructor for class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
 
PointsFitterToMark - Class in org.anchoranalysis.plugin.points.bean.fitter
 
PointsFitterToMark() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
pointsFromContour(ObjectMask) - Static method in class org.anchoranalysis.plugin.points.bean.contour.PointsFromContourTraverser
Extracts a list of points from the outline (contour) of the object-mask
PointsFromContourTraverser - Class in org.anchoranalysis.plugin.points.bean.contour
 
PointsFromMask - Class in org.anchoranalysis.image.core.points
 
PointsFromObject - Class in org.anchoranalysis.image.core.points
 
PointsFromObjects - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
 
PointsFromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
 
PointsFromOrientationProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
 
PointsFromOrientationProposer() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
 
PointsInitParams - Class in org.anchoranalysis.mpp.bean.init
 
PointsNeighborChecker - Class in org.anchoranalysis.image.core.points
 
pointsOnAllOutlines(ObjectCollection) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
 
pointsOnOutline(ObjectMask) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
 
PointsProposer - Class in org.anchoranalysis.mpp.bean.proposer
 
PointsProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PointsProposer
 
PointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
Like a IntConsumer but accepts two coordinates of a point as scalar arguments.
Polygon - Class in org.anchoranalysis.mpp.mark.points
 
Polygon() - Constructor for class org.anchoranalysis.mpp.mark.points.Polygon
 
PolygonCurve - Class in org.anchoranalysis.mpp.mark.points
 
PolygonCurve() - Constructor for class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
populate(List<NamedBean<FeatureListProvider<FeatureInput>>>, Logger) - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
 
populate(PropertyInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
populate(PropertyInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
 
populate(PropertyInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
 
populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle2D
 
populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle3D
 
populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAxisAngle
 
populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory
Populates a newly created matrix.
populateFrom(Stack, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
 
populateMissingFromArbitrarySlice(Stack) - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
 
PopulateStoreFromDefine<V extends BeanInitParams> - Class in org.anchoranalysis.image.bean.nonbean.init
Helps populates a NamedProviderStore from the contents of a Define.
PopulateStoreFromDefine(Define, PropertyInitializer<?>, Logger) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine
Constructor
position() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
The position of the buffer ala Buffer.position.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Assigns a new position to the buffer.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
Assigns a new position to the buffer.
Position - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
Position() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
 
PositionProposer - Class in org.anchoranalysis.mpp.bean.proposer
 
PositionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PositionProposer
 
Positive - Annotation Type in org.anchoranalysis.bean.annotation
The bean-field should have a value > 0.
possibleOverlappingObjects(ObjectMask, Iterable<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
 
possibleOverlappingObjects(ObjectMask, Iterable<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
 
possibleOverlappingObjects(BoundingBox, Iterable<WithConfidence<BoundingBox>>) - Method in class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
As bounding box intersection test is cheap, we pass back all neighbors
possibleOverlappingObjects(T, Iterable<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
Finds a subset of others that possibly overlap with the source element.
precalculate(ObjectWithProperties, Dimensions) - Method in class org.anchoranalysis.overlay.bean.DrawObject
 
precalculate(ColoredOverlayCollection, DrawOverlay, Dimensions, BinaryValuesByte) - Static method in class org.anchoranalysis.overlay.writer.DrawOverlay
 
PrecalculationOverlay - Class in org.anchoranalysis.overlay.writer
Overlays with additional pre-calculations that make them quicker to draw onto a RGBStack
PrecalculationOverlay(ObjectWithProperties) - Constructor for class org.anchoranalysis.overlay.writer.PrecalculationOverlay
 
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
 
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
 
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
 
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
 
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
A precondition, which if evaluates to false, cancels the filter i.e.
precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
 
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
 
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
 
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
 
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
If this evaluates true, the mask will be returned as-is, otherwise maskElse is returned
predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
 
PredicateAtCorner - Class in org.anchoranalysis.image.voxel.extracter.predicate
Projects a VoxelsPredicate to a corner in a larger global space
PredicateAtCorner(ReadableTuple3i, VoxelsPredicate) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
 
PredicateBufferBinary<T> - Interface in org.anchoranalysis.image.voxel.iterator.predicate.buffer
Like ProcessBufferBinary but returns a boolean.
PredicateImplementation<T> - Class in org.anchoranalysis.image.voxel.extracter.predicate
Implementation of VoxelsPredicate for a particular Voxels.
PredicateImplementation(Voxels<T>, Predicate<T>) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
 
PredicateTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.predicate
Like Predicate but takes two bytes as argument.
prefer(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
Prefer to keep descriptor whose input-class is a sub-class rather than a super-class
prefer(Feature<?>, Feature<?>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
Like FeatureInputType.prefer(Class, Class) but accepts features directly as input.
prefixPluralize(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities
Returns n somethings
prefixPluralizeMaybe(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities
Returns 1 something or n somethings as is appropriate
Prepend - Class in org.anchoranalysis.bean.shared.color.scheme
 
Prepend() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Prepend
 
PrependName - Class in org.anchoranalysis.feature.bean.list
Prepends a string to each feature in the list
PrependName() - Constructor for class org.anchoranalysis.feature.bean.list.PrependName
 
PreserveName - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
 
PreserveName() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
 
prettyPath(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.PrettyPathConverter
Converts to either a normalized absolute-path or relative-path depending on which is prettier to the user
prettyPath(Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.PrettyPathConverter
Converts to either a normalized absolute-path or relative-path depending on which is prettier to the user
PrettyPathConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path
 
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
 
previousEqualIndex(int) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncomplete
 
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
 
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
 
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
 
previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
 
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
 
previousIndex(int) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncomplete
 
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
 
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
 
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
 
previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
 
primaryReport() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.StateReporter
 
primaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterIdentity
 
primaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
 
primaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
 
PrimitiveConverter - Class in org.anchoranalysis.image.voxel.buffer.primitive
Type conversion between primitive data types.
PrincipalAxisEccentricity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
Calculates the eccentricity of the Principal Axes (as defined by Image Moments)
PrincipalAxisEccentricity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
 
PrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
The length of a principal-axis (as defined by Image Moments).
PrincipalAxisLength() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
 
PrincipalAxisOrientation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
An element from orientation of a principal-axis (as defined by Image Moments).
PrincipalAxisOrientation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
 
printAllFilesFromTestFolderPath(String) - Method in class org.anchoranalysis.test.TestLoader
Prints the names of all files (recursively) in a test-folder to stdout
PrioritisedVertex - Class in org.anchoranalysis.plugin.image.object.merge.priority
A vertex with a priority attached, and a boolean flag as to whether it can be merged or not
PrioritisedVertex(ObjectMask, double, double, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
Constructor
Prioritizer - Interface in org.anchoranalysis.plugin.image.object.merge.priority
Creates a priority between two vertices
PriorityQueueIndexRangeDownhill<T> - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
Implements a priority queue based upon a range of values from 0 to maxValue,
PriorityQueueIndexRangeDownhill(int) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
 
ProbabilityMap - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
Uses a probability field defined over the voxels to make some positions more likely than others
ProbabilityMap() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
 
probCalculator(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
 
probCalculator(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
 
probCalculator(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
ProbMap - Interface in org.anchoranalysis.mpp.probmap
 
ProbMapObjects - Class in org.anchoranalysis.mpp.probmap
TODO this doesn't seem currently used.
ProbMapObjects(ObjectCollection, Dimensions) - Constructor for class org.anchoranalysis.mpp.probmap.ProbMapObjects
 
ProbWeights - Class in org.anchoranalysis.mpp.probmap
 
ProbWeights() - Constructor for class org.anchoranalysis.mpp.probmap.ProbWeights
 
process(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessTwoBytes
 
process(Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
 
process(Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase
 
process(Channel, Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
 
process(Channel, Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
 
process(VoxelBuffer<S>, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinaryWithoutOffset
Processes a voxel location in a buffer
process(VoxelBuffer<S>, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinary
Processes a voxel location in a buffer
process(VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnary
Processes a voxel location in a buffer.
process(Point3i) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint
 
process(Point3i, VoxelBuffer<S>, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed
Processes a voxel location in two buffers.
process(Point3i, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnaryWithPoint
Processes a voxel location in a buffer.
process(Point3i, S, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary
Processes a voxel location in two buffers.
process(Point3i, T, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary
Processes a voxel location in a buffer
process(Point3i, T, T, T, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary
Processes a voxel location in a buffer
process(S, T) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset
Processes a voxel location in a buffer
process(T) - Method in interface org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP.OperationWithInitParams
 
process(T, EnergyStack) - Method in interface org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy.OperationWithEnergyStack
 
processAllPointsInNeighborhood(boolean, ProcessVoxelNeighbor<?>) - Method in interface org.anchoranalysis.image.voxel.neighborhood.Neighborhood
 
ProcessBufferBinary<S,​T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
Processes a 3D point like ProcessPoint but also retrieves two Buffer for the current z-slice.
ProcessBufferBinaryMixed<S,​T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
Processes a 3D point like ProcessPoint but also retrieves both one VoxelBuffer for the current z-slice and one Buffer for the current z-slice.
ProcessBufferBinaryWithoutOffset<S,​T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
Processes two buffers for each z-slice jointly, without any offset or point.
ProcessBufferTernary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
Processes a 3D point like ProcessPoint but also retrieves three buffers for the current z-slice.
ProcessBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
Processes a 3D point like ProcessPoint but also retrieves a buffer for the current z-slice.
ProcessChangedPointAbsoluteMasked<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor
Processes a point which has been translated (changed) relative to another point - and includes global coordinates and includes an object-mask buffer
processEachSlice(Channel, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper
Applies a Consumer to each slice independently of a Channel.
processEachSlice(BinaryVoxels<UnsignedByteBuffer>, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper
Applies a Consumer to each slice independently of a BinaryVoxels<UnsignedByteBuffer>.
processInput(NamedChannelsForSeries, InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
 
processInput(InputOutputContext, Optional<NamedProvider<Stack>>, Optional<NamedProvider<ObjectCollection>>, Optional<KeyValueParams>, DefineOutputterMPPWithEnergy.OperationWithEnergyStack<MPPInitParams, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy
 
processInput(InputForMPPBean, InputOutputContext, DefineOutputterMPPWithEnergy.OperationWithEnergyStack<ImageInitParams, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy
 
processInput(MultiInput, InputProcessContext<FeatureTableCalculator<T>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
processInput(T, InputProcessContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
 
processInput(T, InputProcessContext<S>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
Processes one input to generate features.
processInputImage(MultiInput, InputOutputContext, DefineOutputterMPP.OperationWithInitParams<ImageInitParams>) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
 
processInputMPP(MultiInput, InputOutputContext, DefineOutputterMPP.OperationWithInitParams<MPPInitParams>) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
 
ProcessOutputOptions - Class in org.anchoranalysis.launcher.options.outputs
Processes command-line options relating to additional outputs.
ProcessOutputOptions(CommandLineExtracter, ExperimentExecutionArguments) - Constructor for class org.anchoranalysis.launcher.options.outputs.ProcessOutputOptions
 
processOverlapping(WithConfidence<ObjectMask>, WithConfidence<ObjectMask>, Runnable, Consumer<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
 
processOverlapping(WithConfidence<T>, WithConfidence<T>, Runnable, Consumer<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
 
processOverlapping(WithConfidence<T>, WithConfidence<T>, Runnable, Consumer<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
Processes an object that is deemed to overlap
processPixel(UnsignedByteBuffer, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityByteBuffer
 
processPixel(UnsignedShortBuffer, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityShortBuffer
 
processPixel(T, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
 
processPoint(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor
Processes a particular point
processPoint(int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute
Processes a particular point
processPoint(int, int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked
Processes a particular point
processPoint(int, int, int, int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
 
ProcessPoint - Interface in org.anchoranalysis.image.voxel.iterator.process
Processes a 3D point.
processStacks(NamedStacks, Optional<String>, GroupedSharedState<Channel, RunningSumChannel>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
 
processStacks(NamedStacks, Optional<String>, GroupedSharedState<Histogram, Histogram>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
 
processStacks(NamedStacks, Optional<String>, GroupedSharedState<S, T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
Processes one set of named-stacks.
ProcessTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.process
Processes two bytes.
ProcessVoxelBufferBinary<S,​T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
Processes a 3D point like ProcessPoint but also retrieves two VoxelBuffers for the current z-slice.
ProcessVoxelBufferBinaryWithoutOffset<S,​T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
Processes two voxel-buffers for each z-slice jointly, without any offset or point.
ProcessVoxelBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
Processes a 3D point like ProcessPoint but also retrieves a VoxelBuffer for the current z-slice.
ProcessVoxelBufferUnaryWithPoint<T,​E extends Exception> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
Processes a 3D point like ProcessVoxelBufferUnary but also exposes a Point3i.
ProcessVoxelNeighbor<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor
Processes a point that is an neighbor of another.
ProcessVoxelNeighborAbsolute<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor
Processes a point that is a neighbor of another - includes global (absolute) coordinates for this point.
ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.iterator.neighbor
 
ProcessVoxelNeighborAbsoluteWithSlidingBuffer(SlidingBuffer<?>) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
ProcessVoxelNeighborFactory - Class in org.anchoranalysis.image.voxel.iterator.neighbor
 
progressing() - Method in interface org.anchoranalysis.core.functional.checked.CheckedSupplier
An interface to a similar supplier that uses a progress-reporter
ProgressReporter - Interface in org.anchoranalysis.core.progress
 
ProgressReporterConsole - Class in org.anchoranalysis.core.progress
 
ProgressReporterConsole(int) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterConsole
 
ProgressReporterIncrement - Class in org.anchoranalysis.core.progress
 
ProgressReporterIncrement(ProgressReporter) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterIncrement
 
ProgressReporterMultiple - Class in org.anchoranalysis.core.progress
 
ProgressReporterMultiple(ProgressReporter, int) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterMultiple
 
ProgressReporterNull - Class in org.anchoranalysis.core.progress
Placeholder that doesn't measure any progress
ProgressReporterOneOfMany - Class in org.anchoranalysis.core.progress
 
ProgressReporterOneOfMany(ProgressReporterMultiple) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
 
ProgressReporterOneOfMany(ProgressReporterMultiple, int, int) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
 
projectMax() - Method in class org.anchoranalysis.image.core.channel.Channel
 
projectMax() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
Maximum-intensity projection.
projectMax() - Method in class org.anchoranalysis.image.core.stack.Stack
Maximum intensity projection.
projectMax() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
Maximum intensity projection.
projectMax() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
A maximum-intensity projection (flattens in z dimension)
projectMax() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
A maximum intensity projection of all slices
projectMean() - Method in class org.anchoranalysis.image.core.channel.Channel
 
projectMean() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
A mean intensity projection of all slices
projectSlice(T) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
 
projectSlice(T) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
 
PropertyDefiner - Interface in org.anchoranalysis.bean.initializable.property
 
PropertyInitializer<P> - Class in org.anchoranalysis.bean.initializable.property
Tries to initialize a bean's property with particular (or derived) parameters
PropertyInitializer(Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.PropertyInitializer
Simpler case where only the current-parameters can be initialized, but for no further property-types.
PropertyInitializer(Class<?>, List<ExtractFromParam<P, ?>>) - Constructor for class org.anchoranalysis.bean.initializable.property.PropertyInitializer
More complex-case where both current-parameters and other extracted property-types can be initialized.
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty
An iterator (of size numPermutations()) with the values for the property
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
 
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
 
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
 
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
 
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
 
propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
 
propertyValuesDefinitelyInteger() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
 
ProposalAbnormalFailureException - Exception in org.anchoranalysis.mpp.proposer
An exception when a proposal could not be made for an abnormal reason
ProposalAbnormalFailureException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException
 
ProposalAbnormalFailureException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException
 
ProposalAbnormalFailureException(Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkProposer
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.mpp.bean.proposer.PointsProposer
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
proposalVisualization(boolean, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ChooseOneList
 
proposalVisualization(boolean, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
 
proposalVisualization(boolean, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrderedList
 
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.proposer.ScalarProposer
 
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
 
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
 
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
 
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
 
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer
 
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.CreateNew
 
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
 
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
 
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
 
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.proposer.OrientationProposer
 
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
 
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
 
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
 
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomXY
 
propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
 
propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
 
propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkProposer
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
 
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ChooseOneList
 
propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
 
propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrderedList
 
propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer
 
propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
 
propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
 
propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
 
propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
 
propose(ProposerContext) - Method in interface org.anchoranalysis.mpp.proposer.OptionalPointProposer
 
propose(ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
 
propose(ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
 
propose(ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
 
propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.mpp.bean.proposer.radii.RadiiProposer
 
propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
 
propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
 
propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.mpp.bean.proposer.PointsProposer
 
propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
 
propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
proposeKernel(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
proposeNewMarks(VoxelizedMarksWithEnergy, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
 
proposeNewMarks(MarksFromPartition, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
 
proposeNewMarks(T, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
 
proposer() - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
 
ProposerBean<T> - Class in org.anchoranalysis.mpp.bean.proposer
 
ProposerBean() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ProposerBean
 
ProposerContext - Class in org.anchoranalysis.mpp.proposer
 
ProposerContext(RandomNumberGenerator, EnergyStack, RegionMap, ErrorNode) - Constructor for class org.anchoranalysis.mpp.proposer.ProposerContext
 
ProposerException - Exception in org.anchoranalysis.mpp.proposer
An exception thrown when something goes wrong in a Proposer
ProposerException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposerException
 
ProposerException(Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposerException
 
ProposerFailureDescription - Class in org.anchoranalysis.mpp.proposer.error
 
ProposerFailureDescription() - Constructor for class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
 
Provider<T> - Interface in org.anchoranalysis.bean.provider
A class (usually an AnchorBean} that creates or provides another obhect
ProviderAsStack - Interface in org.anchoranalysis.image.core.stack
Provides a stack
ProviderHolder<T> - Class in org.anchoranalysis.bean.provider
A convenient way of providing an object without using a AnchorBean.
ProviderHolder(T) - Constructor for class org.anchoranalysis.bean.provider.ProviderHolder
 
put(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
 
put(Class<? extends T>, T) - Method in class org.anchoranalysis.bean.BeanInstanceMap
 
put(String, double) - Method in class org.anchoranalysis.core.value.KeyValueParams
 
put(String, String) - Method in class org.anchoranalysis.core.value.KeyValueParams
 
put(String, CSVRow) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.MapGroupToRow
 
put(ByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Relative put-method from an unsigned byte buffer, represented by a ByteBuffer.
put(ShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Relative put-method from an unsigned short buffer, represented by a ShortBuffer.
put(K, V) - Method in class org.anchoranalysis.core.cache.LRUCache
Puts a key-value pair irrespective of whether its already present or not
put(UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Relative put-method from an unsigned byte buffer, represented by a UnsignedByteBuffer.
put(UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Relative put-method from an unsigned short buffer, represented by a UnsignedShortBuffer.
put(T, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
 
put(U, S) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
 
putAll(KeyValueParams) - Method in class org.anchoranalysis.core.value.KeyValueParams
 
putByte(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
Puts a byte in the buffer at a particular position, converting, if necessary, to the buffer type.
putCode(int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
 
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Puts a double at the current buffer position.
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
 
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
 
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
 
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Puts a double at a particular buffer position.
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
 
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
 
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
 
putDoubleClipped(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Puts a double at the current buffer position, clipping to ensure the value is within the range (0,255).
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Puts a float at the current buffer position.
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
 
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
 
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
 
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Puts a float at a particular buffer position.
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
 
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
 
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
 
putFloatClipped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Puts a float at the current buffer position, clipping to ensure the value is within the range (0,255).
putFloatClipped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Puts a float at the current buffer position, clipping to ensure the value is within the range (0,255).
putIfEmpty(String, double) - Method in class org.anchoranalysis.core.value.KeyValueParams
 
putInt(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
Puts an int in the buffer at a particular position, converting, if necessary, to the buffer type.
putInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
Puts a long at the current buffer position.
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
 
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
 
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
 
putLongClipped(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Puts a long at the current buffer position, clipping to ensure the value is within the range (0,255).
putRaw(byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Puts an unsigned-byte (represented as a byte) at the current buffer position.
putRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Puts an unsigned-int (represented as a int) at the current buffer position.
putRaw(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Puts an unsigned-byte (represented as a byte) a particular buffer position.
putRaw(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Puts an unsigned-int (represented as a int) a particular buffer position.
putRaw(int, short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Puts an unsigned-short (represented as a short) a particular buffer position.
putRaw(short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Puts an unsigned-short (represented as a short) at the current buffer position.
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
Puts an unsigned-byte (represented by an int) at current buffer position.
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
 
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
 
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
Puts an unsigned-byte (represented as a int) a particular buffer position.
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
 
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
 
putUnsigned(int, long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Puts an unsigned-int (represented as a long) a particular buffer position.
putUnsigned(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Puts an unsigned-int (represented by a long) at current buffer position.
putUnsignedClipped(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Puts a long at the current buffer position, clipping to ensure the value is within the range (0,255).
putUnsignedInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Puts an unsigned-int (represented by a int) at current buffer position.
PxlListOperationFromMark - Class in org.anchoranalysis.mpp.feature.bean.mark
 
PxlListOperationFromMark() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.PxlListOperationFromMark
 
PxlMarkMemoFactory - Class in org.anchoranalysis.mpp.mark.voxelized.memo
 

Q

QuadraticEquationSolver - Class in org.anchoranalysis.math.equation
Solves a Quadratic Equation by finding non-complex roots
QuadraticEquationSolver.QuadraticRoots - Class in org.anchoranalysis.math.equation
Roots (solution) of a quadratic equation
QuadraticRoots(double, double) - Constructor for class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
 
quantile(double) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
 
quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
 
quantile(double) - Method in class org.anchoranalysis.math.histogram.Histogram
 
Quantile - Class in org.anchoranalysis.feature.bean.results
The quantile of the results from a particular feature.
Quantile - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
Calculates the threshold value from a quantile of a histogram.
Quantile - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
Quantile() - Constructor for class org.anchoranalysis.feature.bean.results.Quantile
 
Quantile() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
 
Quantile() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
 
quantileAboveZero(double) - Method in class org.anchoranalysis.math.histogram.Histogram
 
QuantileAcrossConnectedComponents - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
Calculates the median of a feature applied to each connected component
QuantileAcrossConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
 
QuantileAcrossObjects<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
Calculates the quantile of a feature applied to each connected component
QuantileAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
 
QuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
 
QuantileIntensity(double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.QuantileIntensity
 
QuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram
Scales by a quantile of the intensity values of an image.
QuantileIntensityFromHistogram(double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
 
QuantileStretch - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data range
QuantileStretch() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
 
QuickBase<T extends InputFromManager> - Class in org.anchoranalysis.plugin.quick.bean.input
A base for quick managers that make various assumptions about file-structure.
QuickBase() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.QuickBase
 
QuickExperiment<S> - Class in org.anchoranalysis.plugin.quick.bean.experiment
A quick way of defining an InputOutputExperiment where several assumptions are made.
QuickExperiment() - Constructor for class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
QuickMultiDatasetExperiment<T extends InputFromManager,​S> - Class in org.anchoranalysis.plugin.quick.bean.experiment
Makes a lot of assumptions, that allows us to reduce the number of inputs to an InputOutputExperiment.
QuickMultiDatasetExperiment() - Constructor for class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
QuickMultiDatasetStructuredExperiment<T extends InputFromManager,​S> - Class in org.anchoranalysis.plugin.quick.bean.structure
Similar to QuickMultiDatasetStructuredExperiment put sets properties according to an expected directory structure.
QuickMultiDatasetStructuredExperiment() - Constructor for class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.Mark
An alternative "quick" metric for overlap for a mark
QuickOverlapCalculation - Interface in org.anchoranalysis.mpp.mark
A method to quickly calculate overlap approximately

R

RadiiMinRatio - Class in org.anchoranalysis.plugin.mpp.bean.check
 
RadiiMinRatio() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
 
radiiOrdered() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
 
radiiOrderedResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
 
RadiiProposer - Class in org.anchoranalysis.mpp.bean.proposer.radii
 
RadiiProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.radii.RadiiProposer
 
RadiiProposerRepeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii
 
RadiiProposerRepeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
 
RadiiRandomizer - Class in org.anchoranalysis.mpp.mark.conic
Utility functions for generating random radii for ConicBase
RadiiRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
 
RadiiRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
 
radiusForRegion(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
radiusForRegionSquared(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
RandomCollection<T> - Class in org.anchoranalysis.mpp.pair
A collection of items from which one can randomly sample
RandomCollection() - Constructor for class org.anchoranalysis.mpp.pair.RandomCollection
 
RandomCollectionWithAddCriteria<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
An implementation of a RandomCollection that uses AddCriteria
RandomCollectionWithAddCriteria(Class<?>) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
randomIndex(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
randomizeRadii(Bound, RandomNumberGenerator, Optional<Resolution>, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.RadiiRandomizer
 
randomMark(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
RandomNumberGenerator - Interface in org.anchoranalysis.core.random
Generates random numbers from various distributions.
RandomNumberGeneratorBean - Class in org.anchoranalysis.bean.shared.random
 
RandomNumberGeneratorBean() - Constructor for class org.anchoranalysis.bean.shared.random.RandomNumberGeneratorBean
 
RandomNumberGeneratorMersenne - Class in org.anchoranalysis.core.random
Implements a random-number generator using the MersenneTwister algorithm.
RandomNumberGeneratorMersenne(boolean) - Constructor for class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
 
RandomOrder - Class in org.anchoranalysis.plugin.io.bean.provider.file
 
RandomOrder() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.RandomOrder
 
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.bound.OrientableBounds
 
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
 
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds
 
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
 
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
 
RandomOrientation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
 
RandomOrientation() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
 
RandomOrientation(RotationBounds) - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
 
RandomXY - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
 
RandomXY() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomXY
 
randOpen(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
A random value between the bounds (open interval)
range() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence
 
Range - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
The range (difference in values) between two quantiles
Range<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range.feature
The statistical range between two values i.e.
Range() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
 
Range() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
 
rangeChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
 
RangeCompareBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
 
RangeCompareBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
 
RangeCompareFromScalars<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
A base-class for setting the boundaries of the range using constant scalars
RangeCompareFromScalars() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
 
rangeCPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
 
rangeLimitsIfEmpty(DefaultCategoryDataset) - Method in class org.anchoranalysis.plot.index.BarPlot
 
rangeLimitsIfEmpty(DefaultBoxAndWhiskerCategoryDataset) - Method in class org.anchoranalysis.plot.index.BoxPlot
 
rangeLimitsIfEmpty(XYDataset) - Method in class org.anchoranalysis.plot.index.LinePlot
 
rangeLimitsIfEmpty(S) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
rangeSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
 
RangeSum - Class in org.anchoranalysis.plugin.annotation.comparison
 
RangeSum() - Constructor for class org.anchoranalysis.plugin.annotation.comparison.RangeSum
 
rangeTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
 
rangeTPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
 
RasterArranger - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
 
RasterArranger() - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.RasterArranger
 
rasterResizing() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
 
RasterTask<S,​U> - Class in org.anchoranalysis.image.experiment.bean.task
An experiment that takes (primarily) a series of raster images as an input.
RasterTask() - Constructor for class org.anchoranalysis.image.experiment.bean.task.RasterTask
 
RasterWriterDelegateBase - Class in org.anchoranalysis.plugin.io.bean.stack.writer
A base class for a StackWriter delegates to another StackWriter based on values of a StackWriteOptions.
RasterWriterDelegateBase() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
 
ratioBounds() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
 
RatioFirstToSecond - Class in org.anchoranalysis.image.feature.bean.object.pair
Ratio of first-object to second-object in a pair
RatioFirstToSecond() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond
 
RatioNonMode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
RatioNonMode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
 
ratioPointsInsideRegion(Mark, List<Point3f>, RegionMap, int) - Static method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
RatioPrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
Calculates the ratio of prinicpal-axis length using Image Moments
RatioPrincipalAxisLength() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
 
RatioThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
 
RatioThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
 
read(Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationReader
Reads an annotation if it can, returns null otherwise
read(Path) - Method in class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationReader
 
read(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
 
ReadableTuple3i - Interface in org.anchoranalysis.spatial.point
Read-only access to a tuple
ReadAnnotationFromFile - Class in org.anchoranalysis.plugin.annotation.bean.strategy
 
readAssumeExists(Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile
 
readCheckExists(Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile
 
readDefaultMarks(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
 
readFile(Path) - Static method in class org.anchoranalysis.io.manifest.file.TextFileReader
 
readFromCSV(Path, boolean) - Static method in class org.anchoranalysis.image.experiment.label.FileLabelMap
 
readFromFile(Path) - Static method in class org.anchoranalysis.core.value.KeyValueParams
 
readMetadata(Path, boolean) - Static method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
Looks for a metadata file describing the resolution
ReadOptions - Class in org.anchoranalysis.io.bioformats.bean.options
 
ReadOptions() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
 
ReadOptionsDelegate - Class in org.anchoranalysis.io.bioformats.bean.options
Forces a particular settings, but otherwise uses settings from a delegate
ReadOptionsDelegate() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
readResolutionXml(File) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXml
Retrieves resolution from a XML file previously written by ResolutionAsXml.writeResolutionXml(Resolution, Path).
ReadVoxelExtentXml - Class in org.anchoranalysis.plugin.io.bean.stack.reader
 
ReadVoxelExtentXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
 
reconstruction(VoxelsWrapper, VoxelsWrapper, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ
 
reconstruction(VoxelsWrapper, VoxelsWrapper, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion
 
reconstruction(VoxelsWrapper, VoxelsWrapper, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
 
record(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
 
recordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
If defined, all output-names that are passed as arguments to both writers are recorded here.
RecordedOutputs - Class in org.anchoranalysis.io.output.recorded
Outputs recorded from RecordOutputNamesForWriter.
RecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputs
 
RecordedOutputsWithRules - Class in org.anchoranalysis.io.output.recorded
Rules to determine what outputting occurs, together with maybe an entity that records the output-names that are used when writing / querying.
RecordedOutputsWithRules() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules
Creates with no rules or outputs defined.
RecordedOutputsWithRules(MultiLevelRecordedOutputs, MultiLevelOutputEnabled, OutputEnabledDelta) - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules
Creates with all elements defined.
recordError(Class<?>, String) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter
Reports an error that occurred as a string
recordError(Class<?>, String) - Method in class org.anchoranalysis.core.log.error.ErrorReporterIntoLog
 
recordError(Class<?>, String) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
 
recordError(Class<?>, Throwable) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter
Reports an error that occurred as an exception
recordError(Class<?>, Throwable) - Method in class org.anchoranalysis.core.log.error.ErrorReporterIntoLog
 
recordError(Class<?>, Throwable) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
 
RecordingWriters - Class in org.anchoranalysis.io.output.recorded
Two writers that record any output-names that are passed as arguments.
RecordingWriters(OutputterChecked, Optional<WriterExecuteBeforeEveryOperation>, Optional<MultiLevelRecordedOutputs>) - Constructor for class org.anchoranalysis.io.output.recorded.RecordingWriters
Creates the two writers.
recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class org.anchoranalysis.io.manifest.operationrecorder.DualWriterOperationRecorder
 
recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in interface org.anchoranalysis.io.manifest.operationrecorder.WriteOperationRecorder
Records a subdirectory that has been recated.
recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.directory.JobRootDirectory
 
recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
 
recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.directory.Subdirectory
 
recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.operationrecorder.DualWriterOperationRecorder
 
recordWrittenFile(String, ManifestDescription, Path, String) - Method in interface org.anchoranalysis.io.manifest.operationrecorder.WriteOperationRecorder
Records a file written.
RecursivelyDescribeExceptionStack - Class in org.anchoranalysis.core.exception.friendly
Generates a nice string representation of an Exception and its causes according to certain rules.
red() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
reduce() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
Reduce the cost matrix by subtracting the smallest element of each row from all elements of the row as well as the smallest element of each column from all elements of the column.
reduce(List<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
 
reduce(List<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElements
Reduce a list of elements (each with a confidence score) to a smaller-list.
reduce(List<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
 
ReduceElements<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
Reduces the number or spatial-extent of elements by favouring higher-confidence elements over lower-confidence elements.
ReduceElements() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElements
 
ReduceElementsGreedy<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
Reduces the number or spatial-extent of elements by favouring higher-confidence elements over lower-confidence elements.
ReduceElementsGreedy() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
 
ReduceFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
Calculates the aggregate of a feature applied to both the first and second objects in a FeatureInputPairObjects.
ReduceFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
 
ReduceRatioFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
Calculates the aggregate of the ratio of first:second and second :first for a FeatureInputPairObjects
ReduceRatioFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
 
Reference<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
 
Reference - Class in org.anchoranalysis.plugin.image.bean.channel.provider
 
Reference - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
 
Reference - Class in org.anchoranalysis.plugin.image.bean.mask.provider
 
Reference - Class in org.anchoranalysis.plugin.image.bean.object.provider
 
Reference - Class in org.anchoranalysis.plugin.image.bean.stack.provider
 
Reference - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
 
Reference - Class in org.anchoranalysis.plugin.points.bean.fitter
 
Reference() - Constructor for class org.anchoranalysis.feature.bean.operator.Reference
 
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
 
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
 
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
 
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference
 
Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
 
Reference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
 
Reference() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.Reference
 
Reference(String) - Constructor for class org.anchoranalysis.feature.bean.operator.Reference
 
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
 
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
 
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
 
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference
 
Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
 
Reference(String) - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
 
ReferencedFeatures<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
 
ReferencedFeatures() - Constructor for class org.anchoranalysis.feature.bean.list.ReferencedFeatures
 
ReferenceFactory - Class in org.anchoranalysis.plugin.image.provider
Creates reference (i.e.
ReferenceOrElse - Class in org.anchoranalysis.plugin.image.bean.object.provider
Returns a object-collection by name if it exists, or else calls objectsElse if it doesn't exist.
ReferenceOrElse() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
 
ReferenceOrEmpty - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
Returns an existing marks-collection or an empty set if it doesn't exist
ReferenceOrEmpty() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
 
referenceString(Object) - Static method in class org.anchoranalysis.core.system.MemoryUtilities
 
ReflectInAxesWithinDistance - Class in org.anchoranalysis.plugin.points.bean.fitter
Reflects points in each axes if all points are within a certain distance from it
ReflectInAxesWithinDistance() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
reflectThroughOrigin() - Method in class org.anchoranalysis.spatial.box.BoundingBox
Reflects the bounding box through the origin (i.e.
RegEx - Class in org.anchoranalysis.bean.shared.regex
The regular-expression to use for matching groups.
RegEx() - Constructor for class org.anchoranalysis.bean.shared.regex.RegEx
 
RegExList - Class in org.anchoranalysis.bean.shared.regex
 
RegExList() - Constructor for class org.anchoranalysis.bean.shared.regex.RegExList
 
RegExMatcher - Class in org.anchoranalysis.plugin.io.bean.descriptivename
 
RegExMatcher() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
 
RegExpFilePathParser - Class in org.anchoranalysis.plugin.io.bean.groupfiles.parser
 
RegExpFilePathParser() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
RegExSimple - Class in org.anchoranalysis.bean.shared.regex
 
RegExSimple() - Constructor for class org.anchoranalysis.bean.shared.regex.RegExSimple
 
RegExSimple(String) - Constructor for class org.anchoranalysis.bean.shared.regex.RegExSimple
 
region() - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks
The region(s) of the marks that specifies the annotation.
region() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
 
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.core.mask.Mask
 
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
A (sub-)region of the voxels.
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
region(BoundingBox, boolean) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
A (sub-)region of the voxels.
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
A (sub-)region of the object-mask.
regionIntersecting(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Creates an object-mask covering the a bounding-box (that is required to intersect at least partially)
regionIntersecting(BoundingBox, int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Like BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially.
RegionMap - Class in org.anchoranalysis.mpp.bean.regionmap
Maps integer IDs to sub-regions in the map
RegionMap() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
RegionMap(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
RegionMapSingleton - Class in org.anchoranalysis.mpp.bean.regionmap
 
RegionMembership - Class in org.anchoranalysis.mpp.bean.regionmap
 
RegionMembership() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
RegionMembership(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
RegionMembershipAnd - Class in org.anchoranalysis.mpp.bean.regionmap
 
RegionMembershipAnd() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
 
RegionMembershipAnd(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
 
RegionMembershipOr - Class in org.anchoranalysis.mpp.bean.regionmap
 
RegionMembershipOr() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr
 
RegionMembershipUtilities - Class in org.anchoranalysis.mpp.bean.regionmap
 
RegionMembershipWithFlags - Class in org.anchoranalysis.mpp.bean.regionmap
 
RegionMembershipWithFlags(RegionMembership, int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
 
regionZ(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Creates an object-mask with a subrange of the slices.
regionZ(int, int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Creates an box with a subrange of the slices.
register(String, AnchorBeanFactory) - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
Registers a specific factory
register(String, CreateFromList<T>) - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
Registers a bean that creates a List<>
registerAllPackageBeanFactories() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
Registers the factories for the beans that exist in this package
registerBeanFactories() - Static method in class org.anchoranalysis.image.bean.RegisterBeanFactoriesImage
 
RegisterBeanFactories - Class in org.anchoranalysis.bean.xml
Utility class for registering the Bean-factories that are found in anchor-bean (or any other)
RegisterBeanFactoriesImage - Class in org.anchoranalysis.image.bean
Registers beans that needs particular factories
rejected() - Method in interface org.anchoranalysis.annotation.mark.DualMarks
The rejected marks.
RejectIfConditionXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
If the XY resolution of an opened-image meets a certain condition then the resolution is scaled by a factor.
RejectIfConditionXYResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
 
RejectIfIntensityLessThan - Class in org.anchoranalysis.plugin.image.feature.bean.score
 
RejectIfIntensityLessThan() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
 
RejectIfNotConnected - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
Rejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components)
RejectIfNotConnected() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
 
RejectIterationIfAllHigh - Class in org.anchoranalysis.image.voxel.object.morphological.accept
 
RejectIterationIfAllHigh() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfAllHigh
 
RejectIterationIfLowDisconnected - Class in org.anchoranalysis.image.voxel.object.morphological.accept
 
RejectIterationIfLowDisconnected() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfLowDisconnected
 
rejectProposal() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
relation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
relation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold
The relation to the threshold to consider
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
 
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
 
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
 
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
 
RelationBean - Class in org.anchoranalysis.bean.shared.relation
 
RelationBean() - Constructor for class org.anchoranalysis.bean.shared.relation.RelationBean
 
RelationToConstant - Class in org.anchoranalysis.bean.shared.relation.threshold
 
RelationToConstant() - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
RelationToConstant(RelationBean, double) - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
RelationToThreshold - Class in org.anchoranalysis.bean.shared.relation.threshold
A threshold and a relation to it, allowing for tests of a value in relation to a threshold.
RelationToThreshold() - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold
 
RelationToValue - Interface in org.anchoranalysis.math.relation
 
RelationWithMatches - Class in org.anchoranalysis.plugin.image.bean.object.filter.dependent
Matches each object with others, and keeps only those where a relation holds true for all matches (in terms of features)
RelationWithMatches() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
relativeMaskTo(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Creates a new object-mask with coordinates changed to be relative to another box.
relativePath() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
 
relativePath() - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
 
relativePath() - Method in class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
 
relativePositionTo(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBox
The relative position of the corner to another bounding box
relativePositionTo(Point3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.box.BoundingBox
 
relativePositionToBox(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBox
A new bounding-box using relative position coordinates to another box
relativeScale(Extent, Extent) - Static method in class org.anchoranalysis.spatial.scale.ScaleFactorUtilities
Calculates a scaling factor so as to scale sdSource to sdTarget
releaseKeepBest() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
 
releaseKeepBest() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
remove() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
 
remove(int) - Method in class org.anchoranalysis.core.color.ColorList
 
remove(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
 
remove(int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
remove(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
remove(int) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
remove(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
remove(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
remove(int) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
remove(int, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
remove(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
remove(EnergySavedInd, int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
remove(MemoCollection, int, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
remove(MemoCollection, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
remove(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
 
remove(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
remove(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
removeAll(Collection<?>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
removeAndUpdateEnergy(VoxelizedMarksWithEnergy, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelDeathPixelized
 
removeAndUpdateEnergy(MarksFromPartition, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelDeathPartition
 
removeAndUpdateEnergy(T, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
 
removeBelowThreshold(int) - Method in class org.anchoranalysis.math.histogram.Histogram
 
removeClosestToUnitZ() - Method in class org.anchoranalysis.math.moment.ImageMoments
 
removeEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
Remove an edge between two vertices.
removeEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
Remove an edge between two vertices.
RemoveExtensions - Class in org.anchoranalysis.plugin.io.bean.descriptivename
Removes extensions from the descriptive-name (but not from the file) AND only if the extension hasn't already been removed upstream.
RemoveExtensions() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
 
RemoveExtensions(FileNamer) - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
 
removeIfExists(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
 
removeIfExists(T) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
removeIntersectingVoxels(ObjectCollection, Dimensions, boolean) - Static method in class org.anchoranalysis.plugin.image.object.ObjectIntersectionRemover
 
RemoveIntersectingVoxels - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
Considers all possible pairs of objects in a provider, and removes any intersecting pixels
RemoveIntersectingVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
 
removeLeft(int) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
Removes the first numToRemove pixels from the left
RemoveMatching - Class in org.anchoranalysis.plugin.io.bean.provider.file
 
RemoveMatching() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
 
removeNonMatching(List<T>) - Method in class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains
 
removeOrReplace(boolean, boolean, boolean) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
Chops of one-side of keep, and one-side of merge
RemoveOverlappingBoundingBoxes - Class in org.anchoranalysis.plugin.image.bean.box
Non-maxima suppression for axis-aligned bounding-boxes using an Intersection over Union score.
RemoveOverlappingBoundingBoxes() - Constructor for class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
 
RemoveOverlappingObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
Non-maxima suppression for object-masks using an Intersection over Union score.
RemoveOverlappingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
 
RemovePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
 
RemovePartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartition
 
RemovePartitionAndThen<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
 
RemovePartitionAndThen() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
 
removePointsInMark(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
removeRight(int) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
Removes the last numToRemove pixels from the right
RemoveTouchingBorder - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
Considers all possible pairs of objects in a provider, and removes those that touch the border.
RemoveTouchingBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
 
removeTouchingBorderXY(Extent) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
RemoveTrailingDirectory - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive
 
RemoveTrailingDirectory() - Constructor for class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
 
removeTwo(int, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
removeTwo(int, int, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
removeTwo(EnergySavedInd, int, int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
removeTwo(MemoCollection, int, int, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
removeVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
Removes a vertex and any edges connected to it.
removeVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
Removes a vertex and any edges connected to it.
RemoveWhitespace - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
Removes any whitespace characters from the path
RemoveWhitespace() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.RemoveWhitespace
 
repeat(int, CheckedRunnable<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
Repeats an operation a number of times.
Repeat - Class in org.anchoranalysis.bean.shared.color.scheme
 
Repeat - Class in org.anchoranalysis.plugin.image.bean.segment.binary
 
Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
 
Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
 
Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
 
Repeat() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Repeat
 
Repeat() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
 
Repeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
 
Repeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
 
Repeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
 
RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel
RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice
Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask
RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
 
RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
 
repeatUntil(int, CheckedBooleanSupplier<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
Repeats an operation until a true value is returned.
repeatWithIndex(int, CheckedIntConsumer<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
Repeats an operation a number of times, passing an increment index to operation each time.
Replace - Class in org.anchoranalysis.plugin.io.bean.path.derive
Generates a file-path by replacing all occurrences of a string-pattern with another
Replace() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Replace
 
replaceBy(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.core.mask.Mask
 
replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
 
replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
 
ReplaceInfinity<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
 
ReplaceInfinity() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceInfinity
 
replaceInput(T) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
Replaces existing input with new input
replaceInputManager(InputManager<?>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
 
replaceInputManager(InputManager<?>) - Method in interface org.anchoranalysis.experiment.io.ReplaceInputManager
 
replaceInputManager(InputManager<?>) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
replaceInputManager(InputManager<?>) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
ReplaceInputManager - Interface in org.anchoranalysis.experiment.io
Indicates and provides a mechanism that the InputManager can be replaced.
ReplaceNaN<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
 
ReplaceNaN() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceNaN
 
replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
 
replaceOutputManager(OutputManager) - Method in interface org.anchoranalysis.experiment.io.ReplaceOutputManager
 
replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
ReplaceOutputManager - Interface in org.anchoranalysis.experiment.io
Indicates and provides a mechanism that the OutputManager can be replaced.
ReplacePropertyBeanFactory<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.xml.factory
Replaces a property (an XML element of attribute) on a bean before loading it
ReplacePropertyBeanFactory(BeanInstanceMap) - Constructor for class org.anchoranalysis.bean.xml.factory.ReplacePropertyBeanFactory
 
replaceSlice(int, VoxelBuffer<FloatBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
 
replaceSlice(int, VoxelBuffer<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
 
replaceSlice(int, VoxelBuffer<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
 
replaceSlice(int, VoxelBuffer<UnsignedShortBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
 
replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
 
replaceSlice(int, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
 
replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.Voxels
Assigns a new buffer for a slice
ReplaceStrategy<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.strategy.replace
 
replaceTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
 
replaceTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
 
replaceTask(Task<T, S>) - Method in interface org.anchoranalysis.experiment.io.ReplaceTask
 
replaceTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
ReplaceTask<T extends InputFromManager,​S> - Interface in org.anchoranalysis.experiment.io
/** Indicates and provides a mechanism that the Task can be replaced.
ReplaceUnusualValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
Calculates the underlying feature, but replaces the result with a constant if it happens to be an "unusual" value
ReplaceUnusualValue() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
 
replaceVoxels(Voxels<?>) - Method in class org.anchoranalysis.image.core.channel.Channel
Assigns new voxels to replace the existing voxels
replaceVoxels(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Replaces the voxels in the object-mask.
replaceVoxels(Voxels<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Replaces the voxels in the box.
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
 
reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
 
reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
 
reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
 
reportBegin(FeedbackBeginParameters<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
 
reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
 
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
 
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
 
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
 
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
 
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
 
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
 
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
 
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
 
reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
 
reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
 
reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
 
reportEnd(FeedbackEndParameters<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
 
reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
 
ReporterAggregate<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
 
ReporterAggregate() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
 
ReporterAggregate(double) - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
 
ReporterException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback
 
ReporterException(String) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.ReporterException
 
ReporterException(Throwable) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.ReporterException
 
ReporterInterval<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
 
ReporterInterval() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
 
ReporterInterval(double) - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
 
ReportFeature<T> - Class in org.anchoranalysis.io.output.bean
 
ReportFeature() - Constructor for class org.anchoranalysis.io.output.bean.ReportFeature
 
ReportFeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
 
ReportFeatureEvaluator() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
 
ReportFeatureForManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
 
ReportFeatureForManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifest
 
ReportFeatureForManifestFileBase - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
 
ReportFeatureForManifestFileBase() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
 
ReportFeatureForMPP<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
 
ReportFeatureForMPP() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
 
ReportFeatureForSharedObjects - Class in org.anchoranalysis.mpp.io.bean.report.feature
 
ReportFeatureForSharedObjects() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForSharedObjects
 
ReportFeatureOnMark - Class in org.anchoranalysis.mpp.io.bean.report.feature
 
ReportFeatureOnMark() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
 
ReportFeatureOnMarks - Class in org.anchoranalysis.mpp.io.bean.report.feature
 
ReportFeatureOnMarks() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
 
ReportFeatureOnObject - Class in org.anchoranalysis.mpp.io.bean.report.feature
 
ReportFeatureOnObject() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObject
 
ReportFeatureOnObjectCollection - Class in org.anchoranalysis.mpp.io.bean.report.feature
 
ReportFeatureOnObjectCollection() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectCollection
 
ReportFeatureOnObjectsBase<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
 
ReportFeatureOnObjectsBase() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
 
ReportFeatureWrapError - Class in org.anchoranalysis.mpp.io.bean.report.feature
 
ReportFeatureWrapError() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
 
reporting(int, StateReporter<T, U>, TransformationContext) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
Reporting<S> - Class in org.anchoranalysis.mpp.segment.optimization.step
Exposes data which is only needed by reporting tools
reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
 
reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
 
reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
 
reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
reportItr(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
 
reportItr(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
 
reportItr(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
 
reportItr(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
 
reportItr(Reporting<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.KernelIterDescriptionSerializerPeriodicReporter
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
 
reportNewBest(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
 
reportNewBest(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
 
reportNewBest(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
 
reportNewBest(Reporting<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
 
RequireArguments - Class in org.anchoranalysis.experiment.bean.require
 
RequireArguments() - Constructor for class org.anchoranalysis.experiment.bean.require.RequireArguments
 
RequireDebugMode - Class in org.anchoranalysis.experiment.bean.require
 
RequireDebugMode() - Constructor for class org.anchoranalysis.experiment.bean.require.RequireDebugMode
 
RequireFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
 
RequireFeatureRelationThreshold() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
reset() - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
 
reset() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
Reset the sum and count to zero
reset() - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection
Resets all items to zero.
reset() - Method in class org.anchoranalysis.math.histogram.Histogram
 
reset() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
 
reset() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
reset() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
reset() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
 
resetInd() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
ResettableCalculation - Interface in org.anchoranalysis.feature.calculate.cache
A calculation that be invalidated (resetted), removing any existing cached value.
resizedXY(int, int, Interpolator) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
resizedXY(int, int, Interpolator) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
Creates a new voxels that are a resized version of the current voxels (only in X and Y dimensions), interpolating as needed.
resizeXY(int, int) - Method in class org.anchoranalysis.image.core.channel.Channel
 
resizeXY(int, int, Interpolator) - Method in class org.anchoranalysis.image.core.channel.Channel
 
resizeXY(Extent) - Method in class org.anchoranalysis.image.core.channel.Channel
 
resizeXY(Extent, Interpolator) - Method in class org.anchoranalysis.image.core.channel.Channel
 
resolution() - Method in class org.anchoranalysis.feature.energy.EnergyStack
The image-resolution asssociated with the energy-stack.
resolution() - Method in class org.anchoranalysis.image.core.channel.Channel
 
resolution() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
Resolution of voxels to physical measurements e.g.
resolution() - Method in class org.anchoranalysis.image.core.mask.Mask
 
resolution() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
resolution() - Method in class org.anchoranalysis.image.core.stack.Stack
 
Resolution - Class in org.anchoranalysis.image.core.dimensions
The resolution of an image.
Resolution() - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution
 
Resolution(double, double, double) - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution
 
Resolution(Tuple3d) - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution
Constructs a resolution from a tuple.
ResolutionAsXml - Class in org.anchoranalysis.plugin.io.xml
Reads and writes a metadata XML file specifying the image-resolution.
resolutionRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
 
resolve(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.Bound
 
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
 
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
 
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
 
resolve(Optional<UnitConverter>, Point3d, Point3d) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
 
resolve(Optional<UnitConverter>, Point3i, Point3i) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
 
resolveArea(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
 
resolveArea(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
Convert area into another unit representation
ResolvedBound - Class in org.anchoranalysis.mpp.bean.bound
A bound resolved into pixel units
ResolvedBound() - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
ResolvedBound(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
ResolvedBound(ResolvedBound) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
ResolvedCalculation<S,​T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.cache
Like a FeatureCalculation but has been resolved against a cache to reuse any existing identical instance.
ResolvedCalculation(FeatureCalculation<S, T>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
 
ResolvedCalculationMap<S,​T extends FeatureInput,​U> - Class in org.anchoranalysis.feature.calculate.cache
A FeatureCalculationMap that has been resolved against a cache.
ResolvedCalculationMap(FeatureCalculationMap<S, T, U, FeatureCalculationException>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
Constructor
resolveDistance(double, Optional<Resolution>, DirectionVector) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
Convert distance into another unit representation
resolveFeatureIdentifier(String) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator
Due to scoping (different prefixes that can exist), an ID needs to be resolved to a unique-string before it can be passed to calculateFeatureByIdentifier
resolveForAxis(Optional<UnitConverter>, AxisType) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
Resolves the distance in a direction aligned to a particular axis
resolveName(String) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
Adds a prefix before the name
resolvePath(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
An absolute path to the prefix
resolvePath(Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
Converts a relative-path to an absolute-path (relative to the file-path associated with this current bean)
resolvePathToCurrentJar(String) - Method in class org.anchoranalysis.launcher.FilePathResolver
 
resolvePathToCurrentJar(Path) - Method in class org.anchoranalysis.launcher.FilePathResolver
 
resolver() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
Returns a resolver for calculations
resolver() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
 
resolveTestPath(String) - Method in class org.anchoranalysis.test.TestLoader
Resolves a path to test-data (relative path to the test-data root) to an absolute path on the file system
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
 
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
 
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueAreaOrVolume
Resolves a measurement of area/volume (in whatever units) to units corresponding to the image pixels/voxels.
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
 
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
 
resolveVolume(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
 
resolveVolume(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
Convert volume into another unit representation
resources() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
Config for resources sued by the launcher
ResourcesConfig - Class in org.anchoranalysis.launcher.config
 
ResourcesConfig(ClassLoader, String, String, String, String) - Constructor for class org.anchoranalysis.launcher.config.ResourcesConfig
 
ResultsVector - Class in org.anchoranalysis.feature.results
A vector of results from feature-calculations.
ResultsVector(int) - Constructor for class org.anchoranalysis.feature.results.ResultsVector
 
ResultsVectorList - Class in org.anchoranalysis.feature.results
A list of elements of type ResultsVector.
ResultsVectorList() - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList
 
ResultsVectorList(ResultsVector) - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList
 
ResultsVectorTestUtilities - Class in org.anchoranalysis.test.feature.plugins
 
ResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature
A results-vector with an optional thumbnail associated with it
ResultsVectorWithThumbnail(ResultsVector) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
 
ResultsVectorWithThumbnail(ResultsVector, Optional<DisplayStack>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
 
ResultsWriter - Class in org.anchoranalysis.feature.io.results
Feature calculation results that can be outputted in different ways.
ResultsWriter(ResultsWriterMetadata, InputOutputContext) - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriter
Creates for metadata and in a particular directory.
ResultsWriterMetadata - Class in org.anchoranalysis.feature.io.results
Additional information needed for the outputs in ResultsWriter.
ResultsWriterMetadata(LabelHeaders, FeatureNameList, ResultsWriterOutputNames) - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
 
ResultsWriterOutputNames - Class in org.anchoranalysis.feature.io.results
The customizable output names used by ResultsWriter, which all follow a pattern based on a prefix.
ResultsWriterOutputNames() - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
Creates using default names, equivalent to a prefix of features.
ResultsWriterOutputNames(String, boolean, boolean) - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
Creates output-names based upon a prefix.
retainAll(Collection<?>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
RetrieveDestinationFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
 
RetrieveDestinationFromDual() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveDestinationFromDual
 
RetrieveDestinationFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
 
RetrieveDestinationFromVoxelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveDestinationFromVoxelized
 
RetrieveSingleMarkOnly - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
Retrieves a mark from a marks, assuming there is only one mark in a marks, otherwise throwing an exception
RetrieveSingleMarkOnly() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
 
RetrieveSourceFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
 
RetrieveSourceFromDual() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveSourceFromDual
 
RetrieveSourceFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
 
RetrieveSourceFromVoxelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveSourceFromVoxelized
 
reuseByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
reuseByte(Voxels<UnsignedByteBuffer>, BinaryValues) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have only two intensity-values representing OFF and ON
reuseInt(Voxels<UnsignedIntBuffer>, BinaryValues) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have only two intensity-values representing OFF and ON
ReuseSingletonStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.replace
Always re-use a singleton SessionInput, invalidating it each time a new call occurs
ReuseSingletonStrategy(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.ReuseSingletonStrategy
Constructor with default means of creating a session-input
ReuseSingletonStrategy(CacheCreator, FindChildStrategy) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.ReuseSingletonStrategy
Constructor with custom means of creating a session-input
reverse() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
 
reversedList(List<Point3i>) - Static method in class org.anchoranalysis.image.core.outline.traverser.visited.ReverseUtilities
 
reverseIterateArray(T[], CheckedConsumer<T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
Iterates through every element in an array in reverse order
ReverseUtilities - Class in org.anchoranalysis.image.core.outline.traverser.visited
 
rewind() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Rewinds the buffer ala ByteBuffer.rewind().
RGB - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
Converts a set of channels to a single RGB-stack.
RGB() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
 
rgbColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
RGBColor - Class in org.anchoranalysis.core.color
 
RGBColor() - Constructor for class org.anchoranalysis.core.color.RGBColor
 
RGBColor(int) - Constructor for class org.anchoranalysis.core.color.RGBColor
 
RGBColor(int, int, int) - Constructor for class org.anchoranalysis.core.color.RGBColor
 
RGBColor(Color) - Constructor for class org.anchoranalysis.core.color.RGBColor
 
RGBColorBean - Class in org.anchoranalysis.bean.shared.color
 
RGBColorBean() - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
 
RGBColorBean(int, int, int) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
 
RGBColorBean(Color) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
 
RGBColorBean(RGBColor) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
 
RGBOutputUtils - Class in org.anchoranalysis.image.core.stack.rgb
 
RGBStack - Class in org.anchoranalysis.image.core.stack.rgb
A stack with exactly three channels, respectively for Red, Green and Blue colors.
RGBStack(Channel, Channel, Channel) - Constructor for class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
RGBStack(Dimensions, ChannelFactorySingleType) - Constructor for class org.anchoranalysis.image.core.stack.rgb.RGBStack
Creates a particularly-sized stack with all channels initialized to 0.
RGBStack(Stack) - Constructor for class org.anchoranalysis.image.core.stack.rgb.RGBStack
Creates from an existing stack (which must have 1 or 3 channels).
rightSize() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
rmv(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
rmvFromUpdatablePairList(ListUpdatableMarkSetCollection, Mark) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
RootDirectory - Class in org.anchoranalysis.io.manifest.directory
 
RootDirectory(Path) - Constructor for class org.anchoranalysis.io.manifest.directory.RootDirectory
 
Rooted - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
Prepend a 'root' before the file-path-prefix obtained from a delegate
Rooted - Class in org.anchoranalysis.plugin.io.bean.path.derive
 
Rooted - Class in org.anchoranalysis.plugin.io.bean.provider.file
Represents a set of files, with a different root depending on the operating-system and conditions.
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
 
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
 
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
 
RootedFilePath - Class in org.anchoranalysis.plugin.io.bean.filepath
 
RootedFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
 
RootedFilePathUtilities - Class in org.anchoranalysis.plugin.io.input.path
 
RootFilePathRegEx - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
 
RootFilePathRegEx() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
 
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
Provides a prefix that becomes the root-folder.
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
 
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
 
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
 
rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
rootFolderPrefixAvoidResolve(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
Provides a prefix that becomes the root-folder.
RootPath - Class in org.anchoranalysis.bean.shared.path
Defines a *root path* i.e.
RootPath() - Constructor for class org.anchoranalysis.bean.shared.path.RootPath
 
RootPathMap - Class in org.anchoranalysis.plugin.io.input.path
A collection of root-paths indexed by their name.
RotatableBoundingBox - Class in org.anchoranalysis.mpp.mark.points
A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.
RotatableBoundingBox() - Constructor for class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
rotate(double) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
RotateAngle2D - Class in org.anchoranalysis.spatial.rotation.factory
 
RotateAngle2D(double) - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotateAngle2D
 
RotateAngle3D - Class in org.anchoranalysis.spatial.rotation.factory
 
RotateAngle3D(double, double, double) - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotateAngle3D
 
RotateAxisAngle - Class in org.anchoranalysis.spatial.rotation.factory
 
RotateAxisAngle(Vector3d, double) - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotateAxisAngle
 
rotatedPoint(double[]) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
rotatedPoint(Point3d) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
rotateOneVectorOntoAnother(Vector3d, Vector3d) - Static method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
RotationBounds - Class in org.anchoranalysis.mpp.bean.mark.bounds
 
RotationBounds() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds
 
RotationBounds2D - Class in org.anchoranalysis.mpp.bean.mark.bounds
Creates a randomly-generated orientation in 2D by uniformally sampling a scalar rotation angle
RotationBounds2D() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
 
RotationBounds3D - Class in org.anchoranalysis.mpp.bean.mark.bounds
Creates a randomly-generated orientation in 3D based upon Euler Angles
RotationBounds3D() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
 
RotationMatrix - Class in org.anchoranalysis.spatial.rotation
A matrix that performs a rotation in Euclidean space.
RotationMatrix(int) - Constructor for class org.anchoranalysis.spatial.rotation.RotationMatrix
 
RotationMatrix(DoubleMatrix2D) - Constructor for class org.anchoranalysis.spatial.rotation.RotationMatrix
 
RotationMatrixFactory - Class in org.anchoranalysis.spatial.rotation.factory
Base for classes that create a RotationMatrix in different ways.
RotationMatrixFactory() - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory
 
RowLabels - Class in org.anchoranalysis.feature.io.csv
Labels for each row of feature-results in the outputted CSV row.
RowLabels(String) - Constructor for class org.anchoranalysis.feature.io.csv.RowLabels
Creates with a single string as an identifier.
RowLabels(Optional<String[]>, Optional<MultiName>) - Constructor for class org.anchoranalysis.feature.io.csv.RowLabels
 
RTree<T> - Class in org.anchoranalysis.spatial.rtree
An R-Tree that contains items, each with an associated bounding-box.
RTree(int) - Constructor for class org.anchoranalysis.spatial.rtree.RTree
Creates an empty R-Tree.
run() - Method in interface org.anchoranalysis.core.functional.checked.CheckedRunnable
 
runCommandLineApp(String[], LauncherConfig, Logger) - Static method in class org.anchoranalysis.launcher.Launch
Runs a command-line app, by parsing arguments
runExperiment(String) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
Runs an experiment identified by an XML found in the resources
runExperiment(String, Optional<String>, Optional<String>) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
Runs an experiment identified by an XML found in the resources
runExperimentInTemporaryFolder(String, Optional<String>, Optional<String>, TemporaryFolder, String[]) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment
runExperimentInTemporaryFolder(String, TemporaryFolder) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment
RunningSum - Class in org.anchoranalysis.math.arithmetic
Mutable class that allows for incrementing jointly sum and count variables, so as to eventually calculate the mean.
RunningSum() - Constructor for class org.anchoranalysis.math.arithmetic.RunningSum
 
RunningSum(double, long) - Constructor for class org.anchoranalysis.math.arithmetic.RunningSum
 
RunningSumCollection - Class in org.anchoranalysis.math.arithmetic
A collection of RunningSum where an operation is executed on all objects in the collection.
RunningSumCollection(int) - Constructor for class org.anchoranalysis.math.arithmetic.RunningSumCollection
Constructor.
RunningSumPoint - Class in org.anchoranalysis.spatial.point
A running sum for tracking points in each dimension
RunningSumPoint() - Constructor for class org.anchoranalysis.spatial.point.RunningSumPoint
 

S

sample(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
sample(RandomNumberGenerator) - Method in interface org.anchoranalysis.mpp.probmap.PointSampler
 
sample(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.probmap.ProbMapObjects
 
sample(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
 
sampleDoubleFromRange(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Generates a uniformly random floating-point number within a range from 0 (exclusive) to endExclusive.
sampleDoubleFromRange(double, double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Generates a uniformly random floating-point number within a range.
sampleDoubleFromZeroCenteredRange(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Generates a uniformly random floating-point number centered around 0 ranging from [-halfWidth,+halfWidth] (both exclusive).
sampleDoubleZeroAndOne() - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Samples from a uniformly-distributed range between 0.0 (exclusive) and 1.0 (exclusive).
sampleDoubleZeroAndOne() - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
 
sampleFromAvailable(int) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
Samples from the available marks
sampleFromList(List<T>) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Samples uniformly an item from a list
sampleInteger(int) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
Samples an integer uniformally between [0..maxVal)
sampleIntFromRange(int) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Generates a uniformly random discrete number within a range from 0 (inclusive) to endExclusive.
sampleIntFromRange(int, int) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Samples from a uniformly random discrete number within a range.
sampleLongFromRange(long) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
Generates a uniformly random discrete number within a range from 0 (inclusive) to endExclusive.
sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.pair.RandomCollection
 
SampleWithDirectory - Class in org.anchoranalysis.plugin.io.bean.provider.file
 
SampleWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
 
ScalarProposer - Class in org.anchoranalysis.mpp.bean.proposer
 
ScalarProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ScalarProposer
 
ScalarThreeDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
Like a IntConsumer but accepts three coordinates of a point as scalar arguments.
ScalarTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
Like a IntConsumer but accepts two coordinates of a point as scalar arguments.
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.Bound
 
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
scale(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
scale(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
scale(double) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
Objects are scaled in pre-rotated position.
scale(double) - Method in class org.anchoranalysis.mpp.mark.Mark
Scales the mark in X and Y dimensions.
scale(double) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
 
scale(double) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
scale(double) - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
scale(double) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
scale(double) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
scale(double) - Method in class org.anchoranalysis.spatial.point.Point2d
 
scale(double) - Method in class org.anchoranalysis.spatial.point.Point2f
 
scale(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
scale(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
scale(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
scale(Channel, ScaleCalculator, Interpolator, MessageLogger) - Static method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
 
scale(Mask, ScaleCalculator) - Static method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
 
scale(ScaleFactor) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Produces a scaled-version of an object-mask.
scale(ScaleFactor) - Method in class org.anchoranalysis.spatial.box.BoundingBox
Scales the bounding-box, both the corner-point and the extent
scale(ScaleFactor, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Produces a scaled-version of an object-mask.
scale(ScaleFactor, Interpolator, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Creates a scaled-version (in XY dimensions only) of the current bounding-box
scale(ScaleFactor, Extent) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
Scales the segmented-objects.
scale(ScaleFactor, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
Scales the bounding-box corner-point, and assigns a new extent
scale(ScaleFactor, Point3i) - Static method in class org.anchoranalysis.spatial.scale.ScaleFactorUtilities
Scales a point in XY (immutably)
Scale - Class in org.anchoranalysis.plugin.image.bean.object.provider
Scales all the objects in the collection by a particular scale-factor.
Scale - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
 
Scale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Scale
 
Scale() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
 
scaleBy(double) - Method in class org.anchoranalysis.math.histogram.Histogram
 
ScaleByMinMaxValue - Class in org.anchoranalysis.plugin.image.bean.channel.convert
Scales by compressing a certain range of values into the 8-bit signal
ScaleByMinMaxValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
 
ScaleByParams - Class in org.anchoranalysis.plugin.image.bean.channel.convert
Scales by compressing a certain range of values into the 8-bit signal
ScaleByParams() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
ScaleByTypeToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert
 
ScaleByTypeToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
 
ScaleCalculator - Class in org.anchoranalysis.image.bean.spatial
 
ScaleCalculator() - Constructor for class org.anchoranalysis.image.bean.spatial.ScaleCalculator
 
ScaleCalculatorConstant - Class in org.anchoranalysis.plugin.image.bean.scale
 
ScaleCalculatorConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
 
ScaleCalculatorInverted - Class in org.anchoranalysis.plugin.image.bean.scale
 
ScaleCalculatorInverted() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
 
ScaleCalculatorMinXYRes - Class in org.anchoranalysis.plugin.image.bean.scale
 
ScaleCalculatorMinXYRes() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
 
ScaleCalculatorRelativeDimensions - Class in org.anchoranalysis.plugin.image.bean.scale
 
ScaleCalculatorRelativeDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
 
scaleClipTo(ScaleFactor, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a containing-extent
ScaledElements<T> - Class in org.anchoranalysis.image.core.object.scale
A list of elements with an object-mask representation that have been scaled.
ScaledMaskCreator - Interface in org.anchoranalysis.overlay.object.scaled
Creates a scaled version of a mask from a mark/object that is not scaled
scaledObjectFor(T) - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements
Gets the scaled version of an element given the unscaled element.
scaleElements(List<T>, ScaleFactor, Extent, AccessObjectMask<T>) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler
Scales every element in a list collectively, ensuring the results remain inside a particular region.
ScaleFactor - Class in org.anchoranalysis.spatial.scale
What to scale x and y dimensions by
ScaleFactor(double) - Constructor for class org.anchoranalysis.spatial.scale.ScaleFactor
 
ScaleFactor(double, double) - Constructor for class org.anchoranalysis.spatial.scale.ScaleFactor
 
ScaleFactorUtilities - Class in org.anchoranalysis.spatial.scale
 
ScaleImage - Class in org.anchoranalysis.plugin.image.task.bean.scale
Task to scale an image.
ScaleImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
scaleObjects(ObjectCollection, ScaleFactor) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler
Scales every object-mask in a collection
scaleObjects(ObjectCollection, ScaleFactor, Optional<UnaryOperator<ObjectMask>>, Optional<UnaryOperator<ObjectMask>>) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler
Scales every object-mask in a collection, allowing for additional manipulation before and after scaling.
scaleObjects(ObjectCollection, ScaleFactor, Extent) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler
Scales every object-mask in a collection, ensuring the results remain inside a particular region.
scaleQuantity(double, int) - Static method in class org.anchoranalysis.spatial.scale.ScaleFactorUtilities
Multiplies a quantity (integer) by a scaling-factor, returning it as an integer
Scaler - Class in org.anchoranalysis.image.core.object.scale
Scales object-masks (or other more generic elements) collectively to avoid undesired overlap.
scaleRadii(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
ScaleToSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack
Create a thumbnail by scales an image to a particular size.
ScaleToSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
 
scaleX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
scaleXY(double) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
Scales the marks in the annotation in X and Y dimensions.
scaleXY(double) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
 
scaleXY(double) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
Scales the mark in X and Y dimensions.
scaleXY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
scaleXY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
scaleXY(double, Extent) - Method in interface org.anchoranalysis.image.core.object.seed.Seed
 
scaleXY(double, Extent) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
scaleXY(double, Extent) - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
 
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.channel.Channel
 
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.mask.Mask
 
scaleXY(ScaleFactor, Interpolator) - Method in class org.anchoranalysis.image.core.channel.Channel
 
ScaleXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Scales the channel in the X and Y dimensions.
ScaleXY - Class in org.anchoranalysis.plugin.image.bean.mask.provider.resize
Scales the mask in XY dimensions, but not in Z dimension.
ScaleXY - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
 
ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
 
ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
 
ScaleXY() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
 
scaleXYBy(ScaleFactor) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
scaleXYBy(ScaleFactor) - Method in class org.anchoranalysis.spatial.Extent
 
scaleXYPoint(Point3d, double) - Static method in class org.anchoranalysis.mpp.mark.MarkWithPosition
 
scaleXYTo(int, int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
scaleY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
sceneContains(Point2i) - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture
 
ScoreObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
 
ScoreObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
 
ScoreVoxels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
Assigns a score (a value indicating how probable something is) to each voxel
ScoreVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
search(FeatureCalculation<S, T>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculationResolver
Searches for an equivalent calculation to calculation
search(FeatureCalculationMap<S, T, U, FeatureCalculationException>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculationResolver
Searches for an equivalent calculation to calculation
second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
 
second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
 
second(String) - Method in interface org.anchoranalysis.io.output.enabled.multi.MultiLevelOutputEnabled
A second-level of OutputEnabled for a particular outputName as used in first-level.
second(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
 
second(String) - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
A RecordedOutputs for recording second-level outputs for a given outputName from the first-level.
Second - Class in org.anchoranalysis.image.feature.bean.object.pair
Evaluates the first-object in a pair only
Second() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second
 
Second(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second
 
SECOND - org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
 
secondaryReport() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.StateReporter
 
secondaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterIdentity
 
secondaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
 
secondaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
 
secondEntries() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
All second-level recorded output entries.
secondLevel(String) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
secondLevelOutputs(String, OutputEnabled) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
 
secondPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
 
secondPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName
The second part of the name.
secondPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
 
Seed - Interface in org.anchoranalysis.image.core.object.seed
A seed provides an voxels that exclusively belong to a particular object, and can be used as a starting hint for segmentation.
SeedCollection - Class in org.anchoranalysis.image.core.object.seed
 
SeedCollection() - Constructor for class org.anchoranalysis.image.core.object.seed.SeedCollection
 
SeedFinderException - Exception in org.anchoranalysis.image.experiment.seed
 
SeedFinderException(String) - Constructor for exception org.anchoranalysis.image.experiment.seed.SeedFinderException
 
SeedFinderException(Throwable) - Constructor for exception org.anchoranalysis.image.experiment.seed.SeedFinderException
 
SeedObjectMask - Class in org.anchoranalysis.image.core.object.seed
 
SeedObjectMask(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.seed.SeedObjectMask
 
seek(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
Seeks a particular slice
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
Segments a channel to produce an object-collection.
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
 
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
 
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
 
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
 
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
 
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
 
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
 
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
 
segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
 
segment(NamedStacks, NamedProvider<ObjectCollection>, Optional<KeyValueParams>, InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
 
segment(NamedStacks, NamedProvider<ObjectCollection>, Optional<KeyValueParams>, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
 
segment(Stack) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled
Segments individually using a pool of size 1 just for one stack
segment(Stack, ConcurrentModelPool<Net>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
 
segment(Stack, ConcurrentModelPool<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled
Segments a stack to produce an object-collection.
segment(Stack, ConcurrentModelPool<T>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
 
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation
Performs a segmentation on voxels so that each voxel has an ON or OFF state after the operation.
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
 
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
 
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
 
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
 
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
 
segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
 
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
 
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask
 
segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask
 
SegmentationBean<T> - Class in org.anchoranalysis.image.bean.segment
Performs some kind of segmentation
SegmentationBean() - Constructor for class org.anchoranalysis.image.bean.segment.SegmentationBean
 
SegmentationFailedException - Exception in org.anchoranalysis.image.bean.nonbean.error
 
SegmentationFailedException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.SegmentationFailedException
 
SegmentationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.SegmentationFailedException
 
SegmentationFailedException(Throwable) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.SegmentationFailedException
 
SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment
Applies a BinarySegmentation algorithm to derive a mask from a channel
SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
 
SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
 
SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
 
SegmentChannelByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
Performs segmentation of a channel using each object in the upstream collection as a mask.
SegmentChannelByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
 
SegmentChannelIntoObjects - Class in org.anchoranalysis.image.bean.segment.object
A base class for algorithms to segment a channel into one or more objects.
SegmentChannelIntoObjects() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
 
SegmentChannelIntoObjectsUnary - Class in org.anchoranalysis.image.bean.segment.object
A base-class for segmentations that takes another object-segmentation algorithm as a parameter.
SegmentChannelIntoObjectsUnary() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
 
SegmentedObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.stack
Objects that are a result of an instance-segmentation.
SegmentedObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
 
SegmentedObjects(List<WithConfidence<ObjectMask>>) - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
 
segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
 
segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
 
segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
 
SegmentInstanceWithModel<T> - Class in org.anchoranalysis.plugin.image.task.bean.segment
Using a model-pool, performs instance segmentation on an image producing zero, one or more objects per image.
SegmentInstanceWithModel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
 
SegmentIntoMarks - Class in org.anchoranalysis.mpp.segment.bean
 
SegmentIntoMarks() - Constructor for class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
 
SegmentMarksFromImage - Class in org.anchoranalysis.plugin.mpp.experiment.bean.segment
Segments an image into a collection of Marks.
SegmentMarksFromImage() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
 
SegmentOnMaximumIntensityAndExpandInZ - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation.
SegmentOnMaximumIntensityAndExpandInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
 
SegmentStack<T> - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
Segments a stack into objects.
SegmentStack() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
 
SegmentStackIntoObjectsPooled<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.stack
A base class for algorithms to segment a stack into one or more objects - using a pool of models (e.g.
SegmentStackIntoObjectsPooled() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled
 
SegmentText - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
Extracts text from a RGB image by using the EAST deep neural network model
SegmentText() - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
 
SegmentThresholdAboveMinBound - Class in org.anchoranalysis.plugin.mpp.bean.segment.binary
 
SegmentThresholdAboveMinBound() - Constructor for class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
 
SegmentWithMarkedPointProcess - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks
Segments a channel with marked pointed processes.
SegmentWithMarkedPointProcess() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
 
SegmentWithSeeds - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
Takes each object one-by-one from objectsSource, and finds matching seeds from objectsSeeds
SegmentWithSeeds() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
 
select(ExperimentExecutionArguments) - Method in class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
 
select(ExperimentExecutionArguments) - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam
Retrieves the parameter.
select(ExperimentExecutionArguments) - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
 
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
 
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks
Takes a stack-collection and extracts a set of references to particular channels (each with a name)
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
 
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
 
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
 
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
 
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
Selects a StackWriter to use as a delegate.
SelectDimensions - Enum in org.anchoranalysis.image.voxel.object.morphological
 
SelectDimensionsFactory - Class in org.anchoranalysis.image.voxel.object.morphological
 
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
 
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator
 
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
 
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
 
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.tabular.CSVGenerator
 
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.text.StringGenerator
 
selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.xml.XMLGenerator
 
SelectFromShared<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
Selects a number of features of shared-features matching against a regular-expression
SelectFromShared() - Constructor for class org.anchoranalysis.feature.bean.list.SelectFromShared
 
selectIndexToRmv(MarkCollection, ProposerContext) - Static method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
 
selective() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
A writer that allows only certain selected output-names, and records the written output-names
selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
 
selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
 
selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
 
selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.UniformRandom
 
selectMarkFrom(MarkCollection, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer
 
selectMarkFrom(MarkCollection, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
 
selectOutputEnabled(Optional<OutputEnabledRules>) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules
Selects which OutputEnabledRules to employ.
SelectParam<T> - Interface in org.anchoranalysis.launcher.executor.selectparam
Different methods of selecting a object T that is used as a parameter for an experiment.
SelectParamFactory - Class in org.anchoranalysis.launcher.executor.selectparam
Creates an appropriate SelectParam based upon the options passed to the command-line.
SelectSlicesBase - Class in org.anchoranalysis.plugin.mpp.bean.region
 
SelectSlicesBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
 
SelectSlicesWithIndexBase - Class in org.anchoranalysis.plugin.mpp.bean.region
 
SelectSlicesWithIndexBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
separate(Collection<T>) - Method in class org.anchoranalysis.spatial.rtree.SpatiallySeparate
Splits the collection of objects into spatially separate clusters, without consuming all elements in elements.
separateConsume(Set<T>) - Method in class org.anchoranalysis.spatial.rtree.SpatiallySeparate
Splits the collection of objects into spatially separate clusters, consuming all elements in elements.
Sequence - Class in org.anchoranalysis.plugin.image.bean.segment.binary
Performs a sequence of succesive segmentations
Sequence() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
 
SequencedDirectory - Interface in org.anchoranalysis.io.manifest.directory.sequenced
 
SequencedDirectoryDeserializer<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced
Applies a deserializer to each file in a directory with a sequence of files.
SequencedDirectoryDeserializer(SequencedDirectory, Deserializer<T>) - Constructor for class org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectoryDeserializer
Creates from a manifest-directory entry.
SequenceInteger - Class in org.anchoranalysis.bean.permute.property
A sequence of integers.
SequenceInteger() - Constructor for class org.anchoranalysis.bean.permute.property.SequenceInteger
 
SequenceMemory - Class in org.anchoranalysis.io.generator.sequence
 
SequenceMemory() - Constructor for class org.anchoranalysis.io.generator.sequence.SequenceMemory
 
SequenceType<T> - Class in org.anchoranalysis.io.manifest.sequencetype
A sequence of elements (of type T), which are mapped to a range of integer indices.
SequenceType() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.SequenceType
 
SequenceTypeException - Exception in org.anchoranalysis.io.manifest.sequencetype
 
SequenceTypeException(Exception) - Constructor for exception org.anchoranalysis.io.manifest.sequencetype.SequenceTypeException
 
SequenceTypeException(String) - Constructor for exception org.anchoranalysis.io.manifest.sequencetype.SequenceTypeException
 
SequentialProcessor<T extends InputFromManager,​S> - Class in org.anchoranalysis.experiment.bean.processor
Executes jobs sequentially
SequentialProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.SequentialProcessor
 
SequentialSession<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
Calculates features with successively different parameters, taking care of caching etc.
SerializedGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
 
SerializedGenerator(Optional<String>) - Constructor for class org.anchoranalysis.io.generator.serialized.SerializedGenerator
 
SerializedObjectSupplier<T> - Interface in org.anchoranalysis.io.manifest.finder
Supplies a serialized-object (if it exists)
serializeObjectToFile(T, Path) - Static method in class org.anchoranalysis.core.serialize.XStreamSerializer
Writes a file with a serialized representation of an object.
SessionInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
Encapsulates a feature-input in the context of a particular session.
SessionInputSequential<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
A feature-input that will be used in a SequentialSession
SessionInputSequential(T, CacheCreator) - Constructor for class org.anchoranalysis.feature.session.SessionInputSequential
Constructor
SessionInputSequential(T, CacheCreator, FindChildStrategy) - Constructor for class org.anchoranalysis.feature.session.SessionInputSequential
 
set() - Method in class org.anchoranalysis.bean.StringSet
 
set(int, double) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
set(int, ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
set(int, Seed) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
set(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
set(int, UpdatableMarkSet) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
setAboveMaxValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
Constant to return if outside the range (above the maximum allowed)
setAcceptNoResolution(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
 
setAcceptOutsideScene(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
 
setAdd(DefineAdderBean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
setAddCriteria(AddCriteria<T>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
setAdditionalBackgrounds(List<DerivePath>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
Additional background-stacks that are possible to use while annotating.
setAdditionalChannels(List<ChannelEntry>) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
Additional channels other than the main one, which are located in the main raster file
setAdditionalChannels(List<ChannelEntry>) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
Additional channels other than the main one, which are located in the main raster file
setAdditionalPropertyPaths(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
Additional property paths that are also changed, along with the main propertyPath *
setAddName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
setAddOne(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
 
setAddSum(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
Added to all gradients (so we can store negative gradients)
setAdjacentChannels(List<AdjacentFile>) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
Channels that are located in a separate raster file adjacent to the main raster file
setAggIntervalLog10(double) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
How many iterations before printing a new report? Encoded in log10.
setAggregateTriggerBank(AggregateTriggerBank<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
setAll(EnergySavedAll) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component
setAngleDegrees(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
 
setAngleRadians(double) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
setAnnealScheme(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
 
setAnnotations(AnnotationInputManager<NamedChannelsInputPart, T>) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
 
setAnnotatorStrategy(S) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
 
setAppendChannels(List<AppendStack>) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
Channels that are located in a separate raster file somewhere else in the project's structure
setAppendCsv(AppendCsv) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
 
setAppendCSV(DerivePath) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
 
setAppendHistogram(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setAppendObjects(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
Appends object-collections to the multi-input
setAppendStack(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setApplyResolution(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
Multiples the values by the x-resolution, if it exists.
setArrange(ArrangeStack) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
 
setArrange(ArrangeStackBean) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
 
setAsMemberFlag(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
 
setAsPercentage(boolean) - Method in class org.anchoranalysis.feature.bean.results.Quantile
If true, the quantile is interpreted as a percentage rather than a decimal
setAssigner(AnnotationComparisonAssigner<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
setAssignMode(AssignMode<S, T, U>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
 
setAvoidBulletOnFirst(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
Iff true no bullet is added for the very first-item in the list
setAvoidDivideByZero(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
 
setAvoidOverlappingObjects(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
If true, no overlapping objects are treated as pairs
setAxis(String) - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
Which axis the unit-vector will align with.
setAxis(String) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
 
setAxis(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
Which axis? X=0, Y=1, Z=2
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
 
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
 
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
 
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
 
setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
Which axis to read from (x,y,z)
setAxis(String) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
 
setAxisColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
setAxisMax(double) - Method in class org.anchoranalysis.plot.AxisLimits
 
setAxisMin(double) - Method in class org.anchoranalysis.plot.AxisLimits
 
setBackground(AnnotationBackground) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
 
setBackground(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
The background.
setBackgroundChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
setBackgroundChannelName(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
setBackgroundChannelProvider(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
setBackgroundColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
setBackgroundID(String) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
setBackgroundStackMap(StringMap) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
If non-null, maps underlying stack-name to a background
setBackgroundStackName(String) - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
 
setBeanExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
setBeanExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
setBelowMinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
Constant to return if outside the range (below the minimum allowed)
setBest(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
 
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
If true uses 8 neighborhood rather than 4 neighborhood etc.
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
if true, uses 8 neighborhood instead of 4, and similarly in 3d
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
 
setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
setBinaryInputChannelID(String) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
The ID of the binary input mask that determines the region of the watershed
setBinarySgmn(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
 
setBirthRepeats(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
 
setBit0(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
setBit1(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
setBit2(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
setBit3(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
setBit4(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
setBit5(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
setBit6(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
setBit7(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
setBitsPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
 
setBlockSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The block-size as per OpenCV implementation (identical default-size)
setBlockStride(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The block-stride as per OpenCV implementation (identical default-size)
setBlue(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
setBlue(int) - Method in class org.anchoranalysis.core.color.RGBColor
 
setBlue(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
setBorderWidth(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
Adds a border around each part of the montage
setBoundCalculator(BoundCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
 
setBoundCalculator(BoundCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
setBounds(RotationBounds) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
 
setBoundsRatio(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
setBoundType(BoundChangeEvent.BoundType) - Method in class org.anchoranalysis.core.index.bounded.BoundChangeEvent
 
setBridgeMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
Used to match each input-object to an intermediary-object
setBundleSize(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
 
setBundleSize(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
setBySlices(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
 
setCacheSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
Size of feature evaluation cache for featureEvaluatorMatch
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
 
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
 
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
Method to calculate the level for a particular object.
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
Calculates the level for the threshold
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
 
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
 
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
 
setCalculateLevelElse(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
 
setCellDefault(ArrangeStackBean) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
setCells(List<Cell>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
setCellSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The cell-size as per OpenCV implementation (identical default-size)
setCenterPoint(Point3d) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
setChangeExisting(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
If true, the existing channel can be changed.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
 
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
 
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
 
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
 
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
 
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
 
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
 
setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
A channel that is provided to the stack.
setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
 
setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
 
setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
 
setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
 
setChannel3(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
 
setChannelAssignFrom(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
 
setChannelConversionStyle(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
To convert as RGB or independently or in another way
setChannelConverter(ConvertChannelTo) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
 
setChannelConverter(ConvertChannelTo) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
Optionally, how to convert from one bit-depth to another (scaling, clipping etc.)
setChannelElse(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
 
setChannelFilter(ChannelFilter) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
Optionally, includes only certain channels when converting.
setChannelFirst(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
Index of first channel
setChannelGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
setChannelID(String) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
The ID of the channel that provides the input to the filter
setChannelIfVoxelZero(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
 
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
 
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
 
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
If either stackAsChannel==true or we have specified additionalChannels this indicated which channel to use from the stack
setChannelLookup(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
 
setChannelMap(ChannelMap) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
setChannelMask(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
If defined, this is the name of channel used as a mask over the values which are fed into the histogram
setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
 
setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
By default all channels are converted into a stack.
setChannelNum(Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
 
setChannelSecond(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
Index of second channel
setChannelsExtra(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
setChannelsPerByteArray(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
 
setChannelThreshold(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
 
setCheck(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
 
setCheckMark(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
setCheckMark(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
 
setCheckMark(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
 
setCheckParsedFilePathBag(CheckParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
Imposes a condition on each parsedFilePathBag which must be-fulfilled if a file is to be included
setClassifierProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
 
setClearOutsideMask(boolean) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
 
setCol(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
 
setCollapseFilename(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
setCollectionID(String) - Method in class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
 
setCollectionID(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
 
setColor(RGBColorBean) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle
The single color to repeat.
setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
An optional color associated with the label when displayed via GUI
setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
 
setColors(List<RGBColorBean>) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList
The list of colors to specify
setColors(ColorScheme) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
The delegate that creates the (unshuffled) list.
setColors(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
Colors to use for drawing objects
setColorScheme(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
 
setColorsUnpaired(ColorScheme) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
setColorUnselectedObjects(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
setColumnDefinition(ColumnDefinition) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
Column definition for the CSVfiles
setColumnFirstNumberPixels(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with the number of pixels for the first Object
setColumnFirstPointX(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with X coordinate of point for the first Object
setColumnFirstPointY(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with Y coordinate of point for the first Object
setColumnFirstPointZ(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with Z coordinate of point for the first Object
setColumnGroup(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
Name of CSV column used to group results (the same values, are outputted together)
setColumnID(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
Name of CSV column with the file identifier
setColumnNumPixels(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
Name of CSV column with the number of pixels for the first Object
setColumnPointX(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
Name of CSV column with X coordinate of point for the first Object
setColumnPointY(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
Name of CSV column with Y coordinate of point for the first Object
setColumnPointZ(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
Name of CSV column with Z coordinate of point for the first Object
setColumns(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
How many columns to use in the montage, or 0 to guess an approximately square output
setColumnSecondNumberPixels(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with the number of pixels for the second Object
setColumnSecondPointX(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with X coordinate of point for the first Object
setColumnSecondPointY(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with Y coordinate of point for the first Object
setColumnSecondPointZ(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
Name of CSV column with Z coordinate of point for the first Object
setCombine(CombineObjectsForFeatures<T>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
setCommand(String) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
One of: open, close, fill, erode, dilate, skel, outline
setComparerLeft(Comparer) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
setComparerRight(Comparer) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
setCondition(KeyValueCondition) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
 
setCondition(KeyValueCondition) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
 
setConfidenceThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
The maximum difference in confidence for merging.
setConstant(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
 
setConstantBound(ResolvedBound) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
 
setContains(String) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
 
setContains(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
A descriptive-name must contain (case-sensitive) this string.
setConvert(ConvertChannelToWithHistogram) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
 
setConvexHull(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
If true, Reduces the set of points by applying a convex-hull operation
setCopyFilesMethod(CopyFilesMethod) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
setCopyFilesNaming(CopyFilesNaming) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
 
setCopyFilesNaming(CopyFilesNaming) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
setCountThreshold(int) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
setCov(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
 
setCreateMark(CreateMarkFromPoints) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
 
setCreateShort(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
 
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
 
setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
If True creates an unsigned short-image
setCsvFilePath(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
 
setCsvIgnoreZeros(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
Iff true, bins with zero-counts are not written as a row in the CSV file.
setCurrentTemp(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
 
setCustomName(String) - Method in class org.anchoranalysis.feature.bean.Feature
An optional additional name that be associated with the feature (defaults to an empty string)
setDatasetName(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
The name of the experiment including version suffix
setDatasetNameSubdirectory(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
If true the datasetName is appended as a subdirectory e.g.
setDatasets(StringSet) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
setDatasets(StringSet) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
setDatasetSpecific(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
setDatasetSpecific(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
setDatasetSuffix(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
A suffix appended to the dataset name extracted from the reg exp
setDatasetVersion(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
A version-suffix appended to the dataset name extracted from the reg exp
setDay(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
If true, the current day (yyyy.MM.dd) is included in the output
setDebug(boolean) - Method in class org.anchoranalysis.bean.shared.path.RootPath
If true this root is preferred, when executing a job in debugging mode
setDebug(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
setDefaultBehaviourString(Optional<String>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
If present, a string is printed in the description if the default-experiment is used, otherwise ignored.
setDefaultColors(ColorScheme) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
The default color-scheme used for outputs, if no other scheme is specified.
setDefine(Define) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
 
setDefine(Define) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
 
setDefine(DefineOutputterMPP) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
setDefine(DefineOutputterMPP) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
setDefine(DefineOutputterMPP) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
setDefine(DefineOutputterMPPWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
setDefine(DefineOutputterMPPWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Adds definitions of stacks/objects etc.
setDelaySizeAtEnd(int) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
setDelegate(ResolvedBound) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
setDelimiter(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
 
setDelta(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
setDeltat(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
 
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
 
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
 
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
 
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
 
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
 
setDestinationFolderPath(FilePath) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
 
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
 
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
 
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
Dimensions to create new mask
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
 
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
 
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
 
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
setDimensionsSource(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
 
setDimensionsTarget(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
 
setDirection(DirectionVectorBean) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
Direction of the distance being converted, defaults to a unit vector along the X-axis
setDirection(VectorInDirection) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
 
setDirectionVector(VectorInDirection) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
 
setDirectory(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
A relative-path (to the user home directory) which is used as an output directory
setDirectory(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
 
setDirectoryDistance(int) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
How many directories to recurse back from the current file to the Experiments/ directory
setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
 
setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
 
setDisablePathModification(boolean) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
 
setDistance(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
setDistance(MarkDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
 
setDistanceMapProvider(ChannelProvider) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
A distance map which can also be used for making decisions on merging
setDistanceMax(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
 
setDistanceTransformMultiplyBy(double) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
Multiplies the distance transform by this factor to make it more meaningful in a short
setDistanceTransformSmoothSigmaMeters(double) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below
setDistanceX(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
setDistanceY(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
setDistanceZ(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
setDistanceZEndIfEmpty(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
setDivideByZeroValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
 
setDivisor(double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
Divide by
setDivisor(int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
What the identifier is divided by to find the modulo.
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
 
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
Whether to perform the morphological dimensions in 3D or 2D
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
 
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
 
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
 
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
 
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
 
setDo3D(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
 
setDummyMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
setElemAllCreator(FeatureListProvider<FeatureInputAllMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
setElement(T) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
 
setElemIndCreator(FeatureListProvider<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
setElemPairCreator(FeatureListProvider<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
setEmptyValue(double) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
 
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
 
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
 
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
 
setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
 
setEmptyValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
 
setEnd(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
An index beyond which we cannot iterate (inclusive)
setEnd(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
 
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
 
setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
 
setEnergyChannelIndexCheck(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
setEnergyChannelIndexFail(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
Index of which channel in the energy-stack to select
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
Index of which channel in the energy-stack to select
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
 
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
The channel that that forms the histogram
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
 
setEnergyIndexGradient(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
 
setEnergyIndexMask(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
A channel of the energyStack that is used as an additional mask using default byte values for ON and OFF
setEnergyIndexMask(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
Optionally, index of another channel that masks the histogram.
setEnergyIndexX(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
setEnergyIndexY(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
setEnergyIndexZ(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
setEnergyParamsName(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
If non-empty, A keyValueParams is treated as part of the energyStack
setEnergySchemeCreator(EnergySchemeCreator) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
 
setEnergySchemeCreator(EnergySchemeCreator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Creates an energy scheme that assigns an energy score to each collection of marks.
setEnergyStack(Optional<EnergyStack>) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
setEnergyStack(EnergyStack) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
 
setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
The pre-annealed total energy
setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
setEquals(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
A descriptive-name must be exactly equal to (case-sensitive) this string.
setErodeAtBoundary(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
 
setError(int, Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
setErrorAll(Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector
 
setErrorDisconnectedObjects(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
If true, throws an error if there is a disconnected object after the erosion
setErrorTree(DefaultTreeModel) - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
 
setExactDepth(int) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
 
setExceptionIfEmpty(boolean) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
If true, then an exception is thrown if the histogram is empty, otherwise is returned.
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
Iff true, zero-valued voxels are excluded from the histogram
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
 
setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
If true, zeros are excluded from considering in the histogram
setExecutionTime(long) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
setExitBeforeOptimization(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Iff true the algorithm exits before optimization begins (useful for debugging).
setExitWithMinima(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
If true, exits early and just returns the minima, without any further segmentation
setExperimentIdentifier(ExperimentIdentifier) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
A name for the experiment.
setExperimentIdentifier(ExperimentIdentifier) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
A folder identifying the type of experiment (where the outputs are all put in the same directory
setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
A folder identifying the type of experiment (where the outputs are all put in the same directory
setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
The value of $1 (see comment above) in naming-structure.
setExpression(String) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
setExtendInZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all slices)
setExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
 
setExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
 
setExtra(double) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
 
setExtractScoreSize(ExtractScoreSize<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
 
setExtractScoreSize(ExtractScoreSize<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
 
setExtractScoreSizeReport(ExtractScoreSize<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
setExtractScoreSizeState(ExtractScoreSize<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
setExtractWeight(ExtractWeightFromMark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
setFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
 
setFactor(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
 
setFactorHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
setFactorLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
setFactorStdDev(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
setFallback(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
setFallbackName(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
If there's no task-name, then this constant is used as a fallback name
setFeature(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
Feature that calculates the score for an object.
setFeature(Feature<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
 
setFeature(Feature<T>) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
 
setFeature(Feature<T>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
The single feature that will be calculated (possibly repeatedly) in the session
setFeature(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
 
setFeature(FeatureListElem<T>) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
The list feature that is duplicated, and populated.
setFeature(FeatureProvider<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
setFeature(FeatureProvider<T>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
setFeatureCondition(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
 
setFeatureCondition(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
Calculates value for the condition - which is checked if it lies within a certain range
setFeatureElse(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
 
setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
 
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
 
setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
 
setFeatureEvaluator(FeatureEvaluator<T>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
 
setFeatureEvaluatorMatch(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
setFeatureEvaluatorMerge(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
 
setFeatureEvaluatorThreshold(FeatureEvaluator<FeatureInputNull>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
Allows merge only if the feature-value satisfies a relation to this threshold
setFeatureListRef(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
 
setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
Features to calculate for objects in the features output.
setFeatures(List<NamedBean<FeatureListProvider<U>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
The features to be exported (after possibly some manipulation or augmentation)
setFeatures(List<FeatureProvider<T>>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
A list of providers, combined together to form a list of features, to be calculated in a session
setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
Features applied to each group to aggregate values (takes FeatureResultsVectorCollection)
setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Additional features that only depend on the image, so do not need to be replicated for every object.
setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Additional features that are processed on the pair of images (i.e.
setFeatureTables(List<OutputFeatureTable>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
Specifies a feature-table that can also be outputted.
setFeedbackReceiver(FeedbackReceiverBean<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Processes feedback from the segmentation algorithm for outputting / debugging.
setFeedbackReceiver(FeedbackReceiverBean<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
 
setFileFilter(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
Files to search for
setFileId(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
Unique identifier for the stack, object-mask-collection etc.
setFileId(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManagerWithFileID
Unique identifier for the stack, object-mask-collection etc.
setFileInput(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
A string indicating the input file(s)
setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
 
setFileInput(NamedFiles) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
setFileName(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
 
setFilenamePrefix(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
 
setFilePath(String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
 
setFilePath(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
 
setFilePath(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
 
setFilePath(Path) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
 
setFilePathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
setFilePathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
 
setFilePathPrefixer(PathPrefixer) - Method in class org.anchoranalysis.io.output.bean.OutputManager
Determines a prefix to use when outputting a file based upon an input-path.
setFilePathPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
 
setFilePathPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
 
setFilePathProviderSVM(FilePathProvider) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
 
setFilePrefix(String) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
setFilesProvider(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
setFilesProvider(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
The files to use as inputs.
setFilesProvider(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
 
setFilesProvider(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
A path to the main channel of each file
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
 
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
 
setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
 
setFilter(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
 
setFilterFilesCsv(MatchedAppendCsv) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
If set, a CSV is read with two columns: the names of images and a
setFindMaxima(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
If true, the maxima of the score is searched for.
setFindOutlinePixelAngle(FindPointOnOutline) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
setFirst(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
Iff true, first object is used, otherwise the second
setFirst(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
Output-names in the first-level.
setFirst(StateTransformerBean<S, U>) - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
First transformation from S to U
setFirstLineHeaders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
setFixRandomSeed(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Iff true uses a constant seed for the random-number-generator (useful for debugging).
setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced
setFolderDataset(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
setFolderOutput(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
setForceBinary(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
setForceChangeBytes(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
setForceDetailedLogging(boolean) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
Whether more detailed log-messages around each experiment occur.
setForceEagerEvaluation(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
setForceReader(String) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
If non-empty forces usage of a particular bioformats plugin
setForceRGB(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
If set, ensures every stack is converted into 3 channels
setForwardDirectionOnly(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
setFrom3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
A sorted-set of three-dimensional integer points from the entire object-mask
setFromOutline(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
 
setGaussian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
If true, the Gaussian filter is included
setGaussianSigmaMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
 
setGradient(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
setGraphColorScheme(PlotColorScheme) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
 
setGrayscaleReconstruction(GrayscaleReconstructionByErosion) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
 
setGreen(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
setGreen(int) - Method in class org.anchoranalysis.core.color.RGBColor
 
setGreen(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
setGroup(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
Specifies a group for the label (similar labels that are displayed together)
setGroup(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
 
setGroup(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
 
setGroup(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
If non-null this file-path is used to determine the group of the file If null, no group is included.
setGroup(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
If defined, translates a file-path into a group.
setGroupNum(int) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
 
setHeight(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
 
setHighestTwoRadiiOnly(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
 
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
 
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
An optional histogram of voxel intensity values which can be used by segment
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
The histogram to plot.
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
setHistogramChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
 
setHistogramIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
setHistogramsExtra(List<HistogramProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
setHistogramsOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not when outputting histograms
setHorizontalAlign(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
 
setId(int) - Method in class org.anchoranalysis.mpp.mark.Mark
 
setId(int) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
 
setId(String) - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
 
setId(String) - Method in class org.anchoranalysis.feature.bean.operator.Reference
 
setId(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
 
setId(String) - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
 
setId(String) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
 
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
 
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
 
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
 
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
 
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
 
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
 
setId(String) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
 
setId(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
ID for the particular object-collection
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
 
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
 
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
 
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
 
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
 
setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
 
setId(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
 
setId(String) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
 
setId(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
Translates an input file name to a unique ID
setIdentifierSuffix(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
setIdentifierSuffix(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
setIdGenerator(DerivePath) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
 
setIdGetter(IdentifierGetter<T>) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
 
setIgnoreAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
 
setIgnoreCase(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
 
setIgnoreContains(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
If non-empty any stackNames (after map) containing a certain string will be ignored
setIgnoreFileNotFoundAppend(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
setIgnoreFittingFailure(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply not included (with only a log error) If false, an exception is thrown
setIgnoreHidden(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
 
setIgnoreHigherSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
 
setIgnoreLowerSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
 
setIgnoreMissingChannel(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
Iff true and we cannot find a channel in the file, we ignore it and carry on
setIgnoreNaN(boolean) - Method in class org.anchoranalysis.feature.bean.operator.Sum
If true, we ignore any NaN values.
setIgnoreNoObjects(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
If true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
setIgnoreRangeAxisOutside(boolean) - Method in class org.anchoranalysis.plot.index.LinePlot
 
setIgnoreZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
 
setImageLabeller(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
Maps a label to an image
setImgChannelMapCreator(ChannelMap) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
setIncludeFeatureNames(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features
setIncludeFileName(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
 
setIncludeFirst(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Include features for the First-object of the pair
setIncludeFolders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
If false, the folders are ignored, and only the file-name is used in the output
setIncludeMerged(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Include features for the Merged-object of the pair
setIncludeSecond(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
Include features for the Second-object of the pair
setIncludeShell(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
setIncludeZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
 
setIncrement(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
Size of step to use when incrementing
setIncrementDegrees(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
 
setIncrementDegrees(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
setIndex(int) - Method in interface org.anchoranalysis.core.index.IndexSetter
 
setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
 
setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
Index in z-dimension of slice to extract
setIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
setIndex(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
setIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
 
setIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
 
setIndex(int) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
Which index to return from the HOG descriptor
setIndex(int, double) - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
Sets an element of the vector by the index of its position, index=0 is the X-element, index=1 is the Y-element etc.
setIndexNonZero(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
setInitContext(OptimizationContext) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
setInitialKernel(Kernel<T>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
setInnerCoreDistance(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
setInPathPrefix(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
 
setInput(InputManager<? extends ProvidesStackInput>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setInput(InputManager<NamedChannelsInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
 
setInput(InputManager<NamedChannelsInputPart>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
The input-manager to specify where/which/how necessary inputs for the experiment occur.
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
 
setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
 
setInput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
 
setInput(MultiInputManager) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
 
setInputDebug(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
 
setInputDirectory(Optional<Path>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
setInputFilterExtensions(Optional<Set<String>>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
If defined, a set of extension filters that can be applied on inputDirectory
setInputFilterGlob(Optional<String>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
If non-null, a glob that is applied on inputDirectory
setInputName(String) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setInputName(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
setInputName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
 
setInputPaths(List<Path>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
setInputPointShift(float) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
setIntensity(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
setInterpolate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
 
setInterpolator(InterpolatorBean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
 
setInterpolator(InterpolatorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
Interpolator used when scaling the background
setInterpolator(InterpolatorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
 
setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
 
setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is removed)
setInverseMask(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
 
setInvert(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
 
setInvert(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
 
setInvert(boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
Iff true, then a file is rejected if regEx matches and vice-versa (opposite to normal behaviour)
setInvertDecisionValue(boolean) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
 
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
 
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
Feature to apply to the histogram
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
Feature to apply to the histogram
setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
Feature to apply to the histogram
setItem(Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
 
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
 
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
 
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
 
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
 
setItem(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
 
setItem(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
 
setItem(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoOne
 
setItem(Feature<S>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
 
setItem(Feature<T>) - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
 
setItem(FeatureListProvider<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.list.PrependName
 
setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
 
setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
For each feature in the list, a corresponding "aggregate" feature is created in the output list
setItem(FeaturePairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
 
setItem(VoxelScore) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
 
setItem(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
 
setItem(ReportFeature<MPPInitParams>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
 
setItem(T) - Method in class org.anchoranalysis.bean.NamedBean
The item that is to be named (i.e.
setItem(T, int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
 
setItem1(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
 
setItem2(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
 
setItemMean(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
 
setItemProportionate(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
 
setItemStdDev(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
 
setIterations(int) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
 
setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
The maximum number of iterations.
setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
 
setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
 
setIterations(int) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
iterations for erode, dilate, open, close
setIterations(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
 
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
The number of dilations and erosions to apply to determine if two objects intersect
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
The number of dilations and erosions to apply and whether to do in the Z dimension
setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
The number of dilations and erosions to apply and whether to do in the Z dimension
setIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
Number of times to perform morphological dilation
setIterationsErosion(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
Number of times to perform morphological erosion
setJobNumber(int) - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
 
setJobShortName(String) - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
 
setKappa(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
 
setKeepEntireImage(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
If true, rather than writing out a bounding-box around the object-mask, the entire image is written
setKeepExtremes(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
setKeepProcessorsFree(int) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
How many processors to avoid using for the tasks.
setKeepProcessorsFree(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
How many processors to avoid using for the tasks.
setKeepZ(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
Keep the z-resolution if it is already defined
setKernel(Kernel<T>) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
 
setKernel(Kernel<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
 
setKernelFactoryList(WeightedKernelList<?>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
setKernelHalfWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
setKernelNegative(KernelPosNeg<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
setKernelPositive(KernelPosNeg<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
setKernelProposer(KernelProposer<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Proposes kernel-changes during iterations of hte marked-point-processes.
setKernelStateBridge(KernelStateBridge<U, T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
 
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
 
setKey(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
 
setKey(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
 
setKeyGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
setKeyLower(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
setKeyMean(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
 
setKeyPrefix(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
Prefix prepended to key
setKeyRequired(boolean) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
setKeyStdDev(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
 
setKeySuffix(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
 
setKeyUpper(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
setKeyValueParamsID(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
 
setKeyValueParamsID(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
If non-empty, the identifier of a key-value-params collection that is passed to the segmentation procedure.
setLabel(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
If true a label is added beside every image showing the slice index
setLabels(List<AnnotationLabel>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
 
setLevel(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
 
setLine(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
 
setList(List<DefineAdderBean>) - Method in class org.anchoranalysis.bean.define.adder.Concatenate
 
setList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
 
setList(List<NamedBean<FromStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
 
setList(List<Provider<Stack>>) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
 
setList(List<RegEx>) - Method in class org.anchoranalysis.bean.shared.regex.RegExList
 
setList(List<StringMapItem>) - Method in class org.anchoranalysis.bean.shared.StringMap
 
setList(List<LoggingDestination>) - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple
The list of loggers to log to
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.Define
 
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
 
setList(List<ObjectFilter>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine
A list of other filters from which the sub-classes implement filtering behaviour.
setList(List<ColorProvider>) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
 
setList(List<ObjectCollectionProvider>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
 
setList(List<BinarySegmentation>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
setList(List<CalculateLevel>) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
 
setList(List<ProviderAsStack>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
 
setList(List<ChannelEntry>) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
 
setList(List<FilesProvider>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Combine
 
setList(List<InputManager<T>>) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
 
setList(List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
 
setList(List<RegionMembership>) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
 
setList(List<AddCriteriaPair>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
 
setList(List<CheckMark>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
 
setList(List<TerminationCondition>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
 
setList(List<FeedbackReceiver<T>>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
 
setList(List<Summarizer<T>>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
 
setList(List<VisitScheduler>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
 
setList(List<VisitScheduler>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
 
setList(FeatureList<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
 
setListAdditionalChannelProviders(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
 
setListAppend(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
setListAppend(List<FilePathBaseAppendToManager>) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
Additional entities that are appended to the multi-input
setListAppendFilePath(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setListAppendKeyValueParams(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setListAppendMarks(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setListAppendMarksFromAnnotation(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setListAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setListAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setListComparers(List<NamedBean<Comparer>>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
 
setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
setListReportFeatures(List<ReportFeature<DeserializedManifest>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
 
setListReportFeatures(List<ReportFeatureForSharedObjects>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
 
setListStackProvider(List<NamedBean<StackProvider>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
The channels we extract the object-masks from - all assumed to be of same dimension
setListStackProviderMIP(List<NamedBean<StackProvider>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
The channels we extract the object-masks from - all assumed to be of same dimension
setLog(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
The logger to use if conditions are fulfilled
setLog(LoggingDestination) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
setLogExperiment(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
Where log messages that do not pertain to a specific job (input) appear.
setLogExperimentPath(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
Relative path to a logger for the experiment in gneeral
setLoggerTaskCreator(LoggingDestination) - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
 
setLogPath(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
if true, the pathIn and pathOut are logged.
setLogTask(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
Where log messages that do pertain to a specific job (input) appear.
setLogTaskPath(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
Relative path to a logger for a specific task
setLookup(StringList) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
 
setMainChannelIndex(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
Index of the mainChannel
setMainChannelName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
The name of the channel provided by the rasters in file Provider
setManifestDescriptionFunction(String) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
 
setManifestDeserializer(ManifestDeserializer) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
setManifestExperimentInputFileSet(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
setManifestFunction(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
 
setManifestFunction(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
setManifestInputFileSet(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
 
setMap(StringMap) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
 
setMarkBounds(MarkBounds) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
 
setMarkBounds(MarkBounds) - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
 
setMarkEvaluator(NamedBean<MarkEvaluator>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
A mark-evaluator that is added to the GUI to support this annotation
setMarkFactory(MarkFactory) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
 
setMarkFactory(MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
 
setMarkFactory(MarkWithIdentifierFactory) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
Creates a new mark, before perhaps further manipulations by a kernel.
setMarkFromMarksProposer(MarkFromCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
setMarkProposer(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
Name of the MarkProposer to use.
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
 
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
 
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
 
setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
 
setMarkProposerAdditionalBirth(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
setMarkProvider(Provider<Optional<Mark>>) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
 
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
 
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
 
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
 
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
 
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
 
setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
 
setMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
The marks
setMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
 
setMarks(Point2d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
setMarksColored(ColoredMarks) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
 
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
 
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
setMarksExplicit(Point3d, Orientation, Point2d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
 
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
setMarksOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not when outputting configurations
setMarksProposer(MarkCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
setMarksProposer(MarkCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
 
setMarksProposer(MarkCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
setMask(Provider<Mask>) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
 
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
 
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
 
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
A mask that is provided to the stack.
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
 
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
 
setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
An optional mask which restricts the algorithm to only parts of the channel where the mask has an ON voxel
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
 
setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
 
setMaskElse(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
Returned instead of mask if the predicate is not satisfied
setMaskFilled(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
setMaskFilled(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
setMaskIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
 
setMaskOutline(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
setMaskValue(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
What voxel value to read as "On" in the mask above.
setMaskValue(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
 
setMatch(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
 
setMatch(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
 
setMatch(RegEx) - Method in class org.anchoranalysis.feature.bean.list.SelectFromShared
 
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
 
setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
 
setMatchString(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
 
setMax(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
setMax(double) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
setMax(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
 
setMax(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
Boundary value indicating maximally-allowed range value
setMax(int) - Method in interface org.anchoranalysis.core.progress.ProgressReporter
 
setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
 
setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
 
setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
 
setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
 
setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
 
setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
 
setMax(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
 
setMax(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
Calculates maximally-allowed range boundary
setMax(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
Maximum-boundary for acceptable range
setMaxCost(double) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
setMaxCost(double) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
setMaxDirectoryDepth(int) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
 
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
An optional maximum distance
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
 
setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
 
setMaxDistanceBetweenMinima(UnitValueDistance) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
 
setMaxDistanceCOG(UnitValueDistance) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
The maximum distance allowed between center-of-gravities of objects
setMaxDistanceDeltaContour(double) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
The maximum distance allowed between two seeds in terms of their values in the distance map
setMaxDistanceDeltaContour(double) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
The maximum distance allowed between the 'distance from contour' values provided from the distanceMap for each point.
setMaxDistanceProposer(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
 
setMaxDistanceZ(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
 
setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
 
setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
 
setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
 
setMaxNumber(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
 
setMaxNumberItems(int) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Limit
 
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
Theoretical maximum number of (CPU) processors to use in parallel.
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
setMaxNumberProcessors(int) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
setMaxNumItems(int) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
 
setMaxNumItems(int) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
 
setMaxSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
setMaxSplitGroups(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
setMaxValue(long) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
 
setMaxVar(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
setMaxVolume(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
 
setMaxX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Maximum X coordinate inclusive
setMaxY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Maximum Y coordinate inclusive
setMaxZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Maximum Z coordinate inclusive
setMean(double) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
Mean
setMedian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
If true, the median filter is included
setMedianRadiusMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
 
setMerge(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
 
setMergedPosTolerance(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
 
setMergeMarkProposer(MarkMergeProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
setMessage(String) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
 
setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
 
setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string for the default).
setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
 
setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
setMin(double) - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
 
setMin(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
Boundary value indicating minimally-allowed range value
setMin(int) - Method in interface org.anchoranalysis.core.progress.ProgressReporter
 
setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
 
setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
 
setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
 
setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
 
setMin(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
 
setMin(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
 
setMin(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
Calculates minimally-allowed range boundary
setMin(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
Minimum-boundary for acceptable range
setMinConfidence(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
The minimum confidence of an element for its object-mask to be included.
setMinConfidence(double) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
Proposed bounding boxes below this confidence interval are removed
setMinDiff(double) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
 
setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
A minimum difference, below which 0.0 is returned
setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
 
setMinDiversity(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
setMinimaImposition(MinimaImposition) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
 
setMinimumBoundingBoxVolume(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
Only objects whose bounding-box volume is greater or equal to this threshold are included.
setMinIntensity(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
 
setMinIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
Intensity for thresholding
setMinIntensityValue(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
setMinMaxIgnoreBeforeIndex(int) - Method in class org.anchoranalysis.plot.index.LinePlot
 
setMinMaxValues(int, int) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
 
setMinNumberObjects(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
setMinNumberPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
If a contour has less than this number of points, we don't split it, and return it as-is
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
Only includes squares that have at lesat this number of voxels
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
 
setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
The minimum number of voxels that must exist in a connected-component to be included.
setMinNumPoints(int) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
 
setMinNumPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
If an object has fewer points than before being fitted, we ignore
setMinNumSlices(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
setMinNumZSlices(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
 
setMinOverlap(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
 
setMinRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
 
setMinRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
 
setMinRadScaleEnd(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
setMinRadScaleStart(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
 
setMinRatio(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
setMinRatioPointsInsideRegion(double) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
setMinSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
 
setMinVal(double) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
setMinVolume(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
 
setMinVolume(UnitValueVolume) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
 
setMinVolumeConnectedComponent(UnitValueVolume) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
 
setMinX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Minimum X coordinate inclusive
setMinXYRes(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
 
setMinY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Minimum Y coordinate inclusive
setMinZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
Minimum Z coordinate inclusive
setMip(boolean) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
 
setMip(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
 
setMip(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
 
setModelDirectory(Path) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
 
setMultipleComparer(MultipleComparer) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
setMultiplyBy(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
setName(String) - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
setName(String) - Method in class org.anchoranalysis.bean.NamedBean
The name associated with item
setName(String) - Method in class org.anchoranalysis.bean.shared.path.RootPath
 
setName(String) - Method in interface org.anchoranalysis.core.identifier.name.NameValue
Sets the associated namme
setName(String) - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
 
setName(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
 
setName(String) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
 
setName(String) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
 
setName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
A name to describe the adjacent file
setName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
The name of the appended entity
setName(S, String) - Method in interface org.anchoranalysis.bean.permute.ApplyPermutations.NameSetter
 
setNameLeft(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
 
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
 
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
Assigns each input a unique compact name.
setNameRight(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
setNavigateHigherDirs(int) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
Search x number directories higher than file
setNewNameOnFeature(Feature<? extends FeatureInput>, String, String) - Static method in class org.anchoranalysis.feature.bean.list.PrependName
 
setNoBlack(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
 
setNormalize(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
 
setNormalize(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
 
setNormalizeFeatures(boolean) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
Normalize features
setNumberChannels(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
 
setNumberColors(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
 
setNumberDilations(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
 
setNumberFrames(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
 
setNumberGPUProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
How many GPU processors to use when this is possible as a substitute for a CPU processor
setNumberLoopPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
 
setNumberPoints(int) - Method in class org.anchoranalysis.plot.index.LinePlot
 
setNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
How many directories to include in the name.
setNumBins(int) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The number of bins in each histogram for a cell
setNumCols(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
setNumDecimalPlaces(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
setNumLeadingZeros(int) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
 
setNumLevelsGrouping(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
setNumMarks(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
 
setNumRep(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
 
setNumRep(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
 
setNumRows(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
setObjectMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
Used to match each intermediary-object to a final-object
setObjects(List<NamedBean<ObjectCollectionProvider>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
setObjects(Provider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
The objects for whom a level is calculated
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
Objects to draw on a background
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
 
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
setObjects(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not when outputting object-collections
setObjects(OutputEnabled) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
setObjects1(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
First collection with items to be merged
setObjects2(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
Second collection with items to be merged
setObjectsBlue(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
 
setObjectsContainer(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
 
setObjectsElse(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
 
setObjectsGreater(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
 
setObjectsGreen(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
 
setObjectsGrouped(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
 
setObjectsLesser(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
 
setObjectsRed(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
 
setObjectsRejected(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
 
setObjectsSave(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
Saves all objects that are inputs to the merge, outputs from the merge, or intermediate merges along the way
setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
 
setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
 
setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
 
setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
 
setObjectsSplitBy(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
 
setObjectsTarget(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
 
setOfConnectedComponentIDs() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
setOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
 
setOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
 
setOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
 
setOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
 
SetOperationFailedException - Exception in org.anchoranalysis.core.index
 
SetOperationFailedException(String) - Constructor for exception org.anchoranalysis.core.index.SetOperationFailedException
 
SetOperationFailedException(Throwable) - Constructor for exception org.anchoranalysis.core.index.SetOperationFailedException
 
setOptimization(OptimizationScheme<VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
The optimization-scheme that determines which configurations are accepted/rejected from one iteration to the next.
setOptionList(List<KernelProposerOption<T>>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
setOptions(ReadOptions) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
 
setOptions(ReadOptions) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
setOrientationProposer(OrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
 
setOrientationXYProposer(OrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
setOutline(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
If true, an outline is drawn around the entries.
setOutlineAtBoundary(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
 
setOutlineColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
The color of the outline
setOutlinePixelsRetriever(OutlinePixelsRetriever) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
setOutlinePixelsRetrieverReverse(OutlinePixelsRetriever) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
setOutlineProvider(MaskProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
 
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
 
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
The width of the outline (only relevant if outline==true
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
The width of the outline.
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
The width of the outline
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
setOutPath(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
Constructs a path as an output, replacing $1, $2 etc.
setOutPathPrefix(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
A directory in which to output the experiment-directory and files
setOutput(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
setOutput(OutputManager) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
The output-manager that specifies how/where/which elements occur duing outputting.
setOutput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
 
setOutputCSV(boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
Iff true, a mapping.csv file is created showing the mapping between the original-names and the anonymized versions
setOutputDirectory(Optional<Path>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
A directory indicating where inputs can be located
setOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not - highest level outputs
setOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
setOutputName(String) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileBase
The name to use (without extension) for the text-file log
setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
 
setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle
An identifier used in rules to determine if an output is enabled or not.
setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
 
setOutputName(String) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
 
setOutputName(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
 
setOutputName(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
setOutputNameStyle(IndexableOutputNameStyle) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
 
setOutputRGBOutline(StringSet) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
setOutputRGBOutlineFlattened(StringSet) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
 
setOutputsDisabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
The names of the outputs that are disbled.
setOutputsEnabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
The names of the outputs that are enabled.
setOutputsEnabled(OutputEnabledRules) - Method in class org.anchoranalysis.io.output.bean.OutputManager
Which outputs are enabled or not enabled.
setOutputShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
Iff true, outputs a short channel, otherwise byte channel
setOutputStackProvider(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
setOutputWriteSettings(OutputWriteSettings) - Method in class org.anchoranalysis.io.output.bean.OutputManager
General settings (default file extensions, colors etc.) for outtping files.
setOutputWriteSettings(OutputWriteSettings) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
setOutside(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
Returned as a constant if a value lies otside the range
setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
 
setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
 
setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
 
setOverlapRatioThreshold(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
setOverlapThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
The maximum size for merging.
setPadding(Padding) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
Padding placed on each side of the outputted image (if it's within the image)
setPaddingXY(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding
Padding placed on each side of the outputted image (if it's within the image) in XY directions
setPaddingZ(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding
Padding placed on each side of the outputted image (if it's within the image) in Z direction
setPairAddCriteria(AddCriteriaPair) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
setPairCollection(RandomCollection<IdentifiablePair<Mark>>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
setPairTypeClass(Class<?>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
setParam(P) - Method in class org.anchoranalysis.bean.initializable.property.PropertyInitializer
Sets the current parameters used for propagation
setParamMean(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
setParamPrefix(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
setParamPrefixAppendNumber(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
If true the constant is appended to the param prefix (a dot and a number)
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
 
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
 
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
 
setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
setParams(KeyValueParams) - Method in class org.anchoranalysis.feature.energy.EnergyStack
 
setParams(HOGParameters) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
Parameters used for calculating HOG
setParams(HOGParameters) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
Parameters used for calculating HOG
setParamStdDev(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
 
setPath(String) - Method in class org.anchoranalysis.bean.shared.path.RootPath
A path on a filesystem to the directory, that defines the root
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
 
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
 
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
 
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
setPathAnnotation(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
 
setPathDefaultMarks(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
setPathLabel(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
Path to a CSV label file (comma-separated, with header, no quotes)
setPathParams(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
setPaths(List<DerivePath>) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
All files need to be present
setPaths(StringSet) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
 
setPenaltyValue(double) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
 
setPeriodTriggerBank(PeriodTriggerBank<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
setPermutation(AnchorBean<?>, Object) - Method in interface org.anchoranalysis.bean.permute.setter.PermutationSetter
 
setPermutation(AnchorBean<?>, Object) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterList
 
setPermutation(AnchorBean<?>, Object) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
 
setPermutation(PermuteProperty<S>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
A permutation to apply.
setPermutations(List<PermuteProperty<S>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
A list of permutations to apply.
setPermuteProperty(PermuteProperty<?>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
 
setPermuteProperty(PermuteProperty<Integer>) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
 
setPermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
 
setPhysical(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
 
setPlotBackgroundColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
setPlotGridlineColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
 
setPoint(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
setPointConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
setPointDirection(Point3i, int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
setPoints(Point3d, Point3d) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
setPoints(Point3i, Point3i) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
setPointsFitter(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
Name of the PointsFitter to use.
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
 
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
 
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
 
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
setPointsFitter(PointsFitterToMark) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
 
setPointsFitter(PointsFitterToMark) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
setPointsFromOrientationProposer(PointsFromOrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
 
setPointsFromOrientationXYProposer(PointsFromOrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 
setPointsProposer(PointsProposer) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
setPos(Point3d) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
 
setPositionProposer(PositionProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
 
setPositionProposer(PositionProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
 
setPower(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
 
setPrefix(boolean) - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
If true, a prefix is prepended to the name of each added bean.
setPrefix(String) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
A prefix that is placed before the name of every bean created
setPrefix(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
 
setPrefix(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
setPrependColor(RGBColorBean) - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
 
setPrependString(String) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
 
setPrependString(String) - Method in class org.anchoranalysis.feature.bean.list.PrependName
 
setPrependString(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
 
setPrependString(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
 
setPreserveExtensionIfDuplicate(boolean) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
Keeps the extension if the file-name (without the extension) becomes duplicated with another
setProbMapID(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
 
setProbNeg(double) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
 
setProbPos(double) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
 
setProperty(String, Object) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
setPropertyPath(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
Either a direct property of a bean e.g.
setProposal(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
 
setProposer(MarkFromCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
 
setProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
 
setProvider(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
 
setPxlPartMemo(MemoCollection) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
 
setPxlPartMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
 
setQuantile(double) - Method in class org.anchoranalysis.feature.bean.results.Quantile
The quantile.
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
 
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
 
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
 
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
 
setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
 
setQuantileHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
 
setQuantileLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
 
setQuantileLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
 
setQuantileUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
 
setRadiiProposer(RadiiProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
 
setRadiiProposer(RadiiProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
 
setRadius(double) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
setRadius(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
 
setRadius(int) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
 
setRadius(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
 
setRadiusBound(Bound) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
 
setRadiusBound(Bound) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
 
setRadiusInMeters(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
 
setRadiusX(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
setRadiusY(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
setRadiusZ(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
setRate(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
 
setReceive(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
 
setRecurseSubfolders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
 
setRecursive(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
Whether to apply the search recursively or not
setRed(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
setRed(int) - Method in class org.anchoranalysis.core.color.RGBColor
 
setRed(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
setReduce(FeatureListElem<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
Method for reducing all pairs into a single value e.g.
setReduce(ReduceElements<ObjectMask>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
The algorithm for reducing the number of object-masks.
setReferencePoissonIntensity(double) - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
setReferencesFeatureListCreator(StringSet) - Method in class org.anchoranalysis.feature.bean.list.ReferencedFeatures
Ensures any feature-lists mentioned here are evaluated, before this list is created.
setReferencesFeatureListCreator(StringSet) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
Makes sure a particular feature list creator is evaluated
setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
 
setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
Regular expression to match against string
setRegex(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
A regular-expression applied to the image file-path that matches three groups.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
 
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
Regular expression to use to match path with at least one group in it.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
 
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
The regular-expression to use for matching groups.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
 
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
If a path matches a regular expression it is removed.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
setRegexAdjacent(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
This needs to be set if there is at least one adjacentChannel.
setRegExDir(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
If non-empty a regular-expression is applied to directories
setRegExFile(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
If non-empty a regular-expression is applied to files
setRegExString(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
The regular-expression to use for matching groups, overloaded to handle legacy situations where a string is supplied.
setRegion(MarkRegion) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
 
setRegion(MarkRegion) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
 
setRegionID(int) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
 
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
 
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.FeatureMarkRegion
 
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
 
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
 
setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
setRegionID(int) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
setRegionMap(RegionMap) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
 
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
 
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
 
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
 
setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
 
setRejectIterationIfAllLow(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
 
setRejectIterationIfDisconnected(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
 
setRelation(RelationBean) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
 
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
Relation to threshold
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
 
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
 
setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
setRemoveExtensionInDescription(boolean) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
Whether to remove the file-extension from the filename.
setRemoveTouchingBorderXY(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
 
setRepeat(int) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
setRepeats(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
Total number of births
setReplaceMatchesWithSolids(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
 
setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
What to replace in the path
setReplacement(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
The replacement string used to determine the file
setReplaceWithMidpoint(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
 
setReportFitterErrors(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
 
setRequireAllFilesMatch(boolean) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
setRequireArguments(RequireArguments) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
The conditions that must be fulfilled
setRequireArguments(RequireArguments) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
 
setRequireBBoxNeighbors(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch
setRequireTouching(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
Requires the object-masks to touch.
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
If set, each channel is scaled to a specific size before the mean is calculated (useful for combining different sized images)
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
The input-image is rescaled to this width/height before calculating HOG descriptors
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
The input is rescaled to this width/height before calculating HOG descriptors
setRestrictTo(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
If set, the inversion only occurs on a particular region of the mask, as determined by this mask
setResX(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
setResY(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
setResZ(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
setRewardHigherSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
Treat the higher side as if it's the the fill cdf
setRewardLowerSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
 
setRgb(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
If true, the output contains three channels (the input and two duplicates) instead of one
setRoot1(double) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
 
setRoot2(double) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
 
setRootInStructure(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
If true the directory structure is ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
 
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
 
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
 
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
 
setRootName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
If non-empty then a rooted filesystem is used with this root
setRootName(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
Root-name assuming multi-rooted strucutre
setRootName(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
 
setRootNameForStructure(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
If rootInStructure==true, the rootName is placed in the folder structure.
setRotateOnlyIn2DPlane(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
 
setRotationAngle(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
 
setRotationAngle(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
 
setRotationBounds(RotationBounds3D) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
 
setRotationX(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
 
setRotationY(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
 
setRotationZ(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
 
setRotMatrix(DoubleMatrix2D) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
setRow(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
 
setSampleEvery(int) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
 
setScalarProposer(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
 
setScalarProposer(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
 
setScale(double) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
Standard-Deviation
setScale(double) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
Whether to increase or reduce the size of the images
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
 
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
Determines how much to scale by
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
 
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
 
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
 
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
 
setScaleFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
 
setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
Sets the min by multiplying the quantileLower by this constant.
setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
setScaleRadii(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
Sets the max by multiplying the quantileUpper by this constant.
setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
 
setScore(VoxelScore) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
 
setScoreProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
setScoreThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
Bounding boxes with scores above this threshold are removed
setSecond(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
Only relevant if time==true.
setSecond(List<NamedBean<StringSet>>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
Output-names in the second-level (for all first level output-names)
setSecond(StateTransformerBean<U, T>) - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
Second transformation from U to T
setSecondary(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
If proposal is true, this toggles between the primary and secondary proposal
setSecondary(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
 
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
 
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
Segmentation algorithm
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
 
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
 
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
 
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
 
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
 
setSegment(SegmentIntoMarks) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
How to perform the segmentation.
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
The segmentation procedure.
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
The segmentation algorithm
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
The segmentation algorithm that is applied as an input to non-maxima suppression.
setSegmentStack(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
 
setSelect(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
Either "merged" or "first" or "second" indicating which feature to delegate from
setSelectChannels(FromStacks) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
Selects which channels are included, optionally renaming.
setSeperator(String) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
 
setSeperator(String) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
setSequence(SequenceInteger) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence
Where the sequence starts
setSequence(SequenceInteger) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
First number range that is appended
setSequence(OutputSequenceIndexed<T, S>) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
 
setSequenceAdditional(SequenceInteger) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
Another number range that is appended
setShellRad(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
 
setShellRad(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
 
setShellRad(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
setShellRad(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
setShellRad(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
setShellRad(double) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
 
setShellRad(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
setShift(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
 
setShowAgg(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
 
setShowBest(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
 
setShowDomainAxis(boolean) - Method in class org.anchoranalysis.plot.index.BarPlot
 
setShowOngoingJobsLessThan(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
setShowVerticalAxisLines(boolean) - Method in class org.anchoranalysis.plot.PlotInstance
 
setSigma(double) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
 
setSigma(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
 
setSigmaInMeters(boolean) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
 
setSilentlyDeleteExisting(boolean) - Method in class org.anchoranalysis.io.output.bean.OutputManager
Whether to silently first delete any existing output at the intended path, or rather throw an error.
setSilentlyDeleteExisting(boolean) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
setSimplePairCollectionID(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
setSize(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
setSize(int) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
 
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
Size of the image produced showing a plot of the histogram
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
Size of all created thumbnails
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
 
setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
setSkipAtBorder(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
If true we do not fill any objects that touch the border
setSkipFileName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
Iff true the filename is not considered, only the subdirectories.
setSkipFileName(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
setSkipFirstTrim(int) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
 
setSkipFirstTrim(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
setSkipMissingChannels(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
setSkipNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
Initially skip this number of directories before including them in the description.
setSlice(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
 
setSliceEnd(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
 
setSliceFirst(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
First slice.
setSliceID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
Index of slice to use, or -1 to use all slices
setSliceIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
Which slice to use from mask
setSliceLast(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
Last slice.
setSliceNum(Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
 
setSlicesSeparately(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
 
setSliceStart(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
 
setSmoothingFactor(double) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
 
setSource(String) - Method in class org.anchoranalysis.bean.shared.StringMapItem
 
setSource(FeatureSource<T, S, U>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
Source of feature-values to be exported
setSourceFolderPath(FilePath) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
setSplitDescriptiveNameRegex(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
setSplitProposer(MarkSplitProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
setSquareSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
 
setStack(Provider<Stack>) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
 
setStack(StackProvider) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
The stack that is the background for our objects
setStack(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
setStack(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
 
setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
Provides a stack.
setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
The stack to segment
setStackAsChannel(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no additionalChannel is set)
setStackBackground(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
setStackEnergy(Provider<Stack>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
Optionally specifies an energy-stack to be associated with every calculation input.
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks)
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
 
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
 
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
 
setStackID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
 
setStackName(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
If defined, processing only occurs the stack with this specific stack and index.
setStackNameVisualOriginal(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
 
setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
Specifies the ID of an existing stack.
setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
 
setStackReader(StackReader) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
 
setStackReader(StackReader) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
 
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
The raster-reader for reading the main file
setStackReaderAdjacent(StackReader) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
The raster-reader to use for opening any adjacent-channels
setStackReaderAppend(StackReader) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
The raster-reader for reading any appended files
setStackReaderHigh(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
setStackReaderInput(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
setStackReaderLow(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
setStackReaderMiddle(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
setStacksOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
Deprecated.
What's allowed or not when outputting stacks
setStacksOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
setStart(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
The index to begin iteration from
setStartIndex(int) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
setStartingIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
The first intensity-value to consider as a valid object (e.g.
setStateReporter(StateReporter<T, S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
setStrategy(BlurStrategy) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
 
setStrongEdgeEnhancer(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
Enables the StrongEdgeEnhancer diffusion function
setSubdirectory(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
If non-empty than an additional subdirectory is appended as a suffix ${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
setSubDirectory(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
 
setSubtractConstant(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
 
setSubtractFromMaskOnly(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
 
setSubtractRadii(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
 
setSuffix(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
 
setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
 
setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
 
setSummarizerElse(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
Used for summary if count(elements) <= countThreshold
setSummarizerGreaterThan(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
Used for summary if count(elements) > countThreshold
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
 
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
 
setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
 
setSuppressErrors(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
 
setSuppressExceptions(boolean) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
 
setSuppressExceptions(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
setSuppressExceptions(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
setSuppressOutlineZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
if true, the outline is suppressed in the z-dimension i.e.
setSuppressRes(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
 
setSuppressRootOut(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.
setSuppressSeries(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
If true, the series index is not included in the outputted file-names.
setSuppressSubfolders(boolean) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
 
setSuppressZ(boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
 
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
 
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
 
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
 
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
 
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
If true co-voariance is suprpessed in z-dimension
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
 
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
 
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
 
setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
Iff true, surpresses covariance in the z-direction.
setSuppressZCovariance(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
 
setSuppressZCovariance(boolean) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
 
setTarget(String) - Method in class org.anchoranalysis.bean.shared.StringMapItem
 
setTask(Task<MultiInput, S>) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
setTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
 
setTask(Task<T, S>) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
setTask(Task<T, S>) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
setTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
 
setTask(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
 
setTaskName(Optional<String>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
A name to describe the ongoing task
setTaskProcessor(JobProcessor<T, S>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
What task is associated with the experiment, and how it is processed.
setTemperature(double) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
 
setTemplateMark(MarkFactory) - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
 
setTermination(TerminationCondition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
 
setThreshold(double) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
setThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
setThreshold(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold
Only considers values greater or equal to the threshold
setThreshold(double) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
 
setThreshold(double) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
 
setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
 
setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
 
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
 
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
 
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
 
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
 
setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
 
setThreshold(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
 
setThreshold(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
 
setThreshold(UnitValueVolume) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
 
setThresholder(Thresholder) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
 
setThresholder(Thresholder) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
The thresholder that will convert a channel into a binary-channel
setThresholdHigh(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
setThresholdLow(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
setThrowExceptionForInsufficientPoints(boolean) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
 
setThumbnail(ThumbnailFromObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
Generates a thumbnail representation of one or more objects combine, as form a single input
setThumbnail(ThumbnailFromStack) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
Method to generate a thumbnail for images
setTime(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
If true, the current time (HH.mm.ss) is included in the output
setTimeIndex(int) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
 
setTimeIndex(Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
 
setTimeIndexGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
setTimes(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
 
setTitle(String) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
 
setTitle(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
 
setToleranceLog10(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
 
setTransformer(StateTransformerBean<MarkCollection, T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
 
setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
 
setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
 
setTransformerKernelToState(StateTransformerBean<U, T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
 
setTransformerMarks(StateTransformerBean<MarkCollection, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
 
setTransformerPrimary(StateTransformerBean<T, S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
 
setTransformerSecondary(StateTransformerBean<T, S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
 
setTransformerStateToKernel(StateTransformerBean<T, U>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
 
setTransposed(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
 
setTrimTrailingDirectory(int) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
 
setTrimTrailingDirectory(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
 
setUniqueLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
Label that uniquely identifies the ID (for machine purposes)
setUnit(UnitConverter) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
 
setUnit(UnitConverter) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
 
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
 
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
 
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
 
setUnitType(String) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
 
setUnitType(String) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
 
setUnitTypeFrom(String) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
 
setUnitTypeTo(String) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
 
setUnitValueDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
 
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo
Always called before any batch of calls to ConvertTo.convertSliceOfSingleChannel(java.nio.ByteBuffer, int).
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
 
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
 
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
 
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
 
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
 
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
 
setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
 
SetUpdatable - Class in org.anchoranalysis.mpp.bean.points.updatable
 
SetUpdatable() - Constructor for class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
setupParams(KeyValueParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
 
setupParams(KeyValueParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
 
setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
 
setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
 
setUseMax(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
 
setUseMax(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
 
setUseMIP(boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
 
setUseMIP(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
 
setUserFriendlyLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
Descriptive user-friendly label displayed via GUI
setUseZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
 
setUseZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
setValue(double) - Method in class org.anchoranalysis.feature.bean.operator.Constant
 
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
 
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
 
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
 
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
 
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
 
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
 
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
 
setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
 
setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
 
setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
 
setValue(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
 
setValue(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
 
setValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
 
setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
 
setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
 
setValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
 
setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
 
setValue(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
 
setValue(T) - Method in class org.anchoranalysis.bean.NamedBean
 
setValue(T) - Method in interface org.anchoranalysis.core.identifier.name.NameValue
Sets the associated value
setValue(V) - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
 
setValueByDimension(int, double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
setValueByDimension(int, float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
setValueIfEmpty(double) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
The value to return iff exceptionifEmpty is false
setValueIfTooFewVoxels(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate moments
setValueNoObject(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
 
setValueNoObjects(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
 
setValues(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
 
setValues(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
The values of the string-set
setVaryColors(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
If true the colors change for different objects in the image (using a default color set).
setVersion(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
 
setVerticalAlign(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
 
setVisitScheduler(VisitScheduler) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
setWeight(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
 
setWeightBackground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
setWeightForeground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
 
setWeightItem1Greater(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
 
setWeightItem2Greater(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
 
setWeightNegative(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
setWeightPositive(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
 
setWeightWidthDescription(int) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
 
setWhenDetailed(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
Logger to use when detailed-logging is on
setWhenEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
setWhenNot(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
Logger to use when detailed-logging is off
setWhenNotEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
 
setWhenOneOrThreeChannels(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
Writer employed if a stack is a one or three-channeled image, that is not 3D, and not RGB.
setWhenRGB(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
Writer employed if a stack is a three-channeled RGB image and is not 3D.
setWidth(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
Width (what the difference is divided by)
setWidth(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
 
setWidthFactor(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
 
setWindowSize(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
 
setWindowSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
The window-size as per OpenCV implementation.
setWithin(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
Returned as a constant if a value lies within the range
setWithinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
Constant to return if value lies within the range
setWithinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
Constant to return if value lies within the range
setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
Default writer, if a more specific writer is not specified for a condition.
setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
 
setWriterAlways2D(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
Writer to use if it is guaranteed that the image will always be 2D.
setWriterElse(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
Otherwise the writer to use.
setWriters(List<NamedBean<?>>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
setX(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
setX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
setX(int) - Method in class org.anchoranalysis.spatial.point.Point2i
 
setX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
setX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
setX(String) - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
 
setXY(String, String) - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
 
setY(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
setY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
setY(int) - Method in class org.anchoranalysis.spatial.point.Point2i
 
setY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
setY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
setY(String) - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
 
setYAxisLowerMargin(double) - Method in class org.anchoranalysis.plot.index.LinePlot
 
setYAxisMargins(double) - Method in class org.anchoranalysis.plot.index.LinePlot
 
setYAxisUpperMargin(double) - Method in class org.anchoranalysis.plot.index.LinePlot
 
setYValGetter(LinePlot.YValGetter<T>) - Method in class org.anchoranalysis.plot.index.LinePlot
 
setZ(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
setZ(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
setZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
setZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
setZAlign(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
 
setZOnly(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
 
setZSliceGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
 
setZSliceNum(int) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
 
SgmnMPPState - Class in org.anchoranalysis.plugin.mpp.segment
 
SgmnMPPState(KernelProposer<VoxelizedMarksWithEnergy>, Define) - Constructor for class org.anchoranalysis.plugin.mpp.segment.SgmnMPPState
 
shallowCopy() - Method in class org.anchoranalysis.core.color.ColorList
 
shallowCopy() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
Creates a new graph with identical elements and structure, reusing the existing vertice and edge data objects.
shallowCopy() - Method in class org.anchoranalysis.feature.name.FeatureNameList
 
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
 
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
Make a shallow copy
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
Creates a shallow-copy of the marks
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
 
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
shallowCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
shallowCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
shallowCopy() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
shallowDuplicate() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
Creates a new feature-list which contains identical elements
ShapeRegularityCenterSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
 
ShapeRegularityCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
 
ShapeRegularityMIP - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
 
ShapeRegularityMIP() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMIP
 
SharedFeatureMulti - Class in org.anchoranalysis.feature.shared
A group of features (of possibly heterogeneous type) made available to other features to reference
SharedFeatureMulti() - Constructor for class org.anchoranalysis.feature.shared.SharedFeatureMulti
 
SharedFeatureSet<T extends FeatureInput> - Class in org.anchoranalysis.feature.shared
 
SharedFeatureSet(NameValueSet<Feature<T>>) - Constructor for class org.anchoranalysis.feature.shared.SharedFeatureSet
 
SharedFeaturesInitParams - Class in org.anchoranalysis.feature.shared
 
SharedObjects - Class in org.anchoranalysis.core.identifier.provider.store
Objects shared between different components.
SharedObjects(CommonContext) - Constructor for class org.anchoranalysis.core.identifier.provider.store.SharedObjects
 
sharedObjectsRequired() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
 
SharedStateExportFeatures<S> - Class in org.anchoranalysis.plugin.image.task.feature
Shared-state for an export-features class
SharedStateExportFeatures(ResultsWriterMetadata, Supplier<S>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
Creates the shared state.
SharedStateFilteredImageOutput<T> - Class in org.anchoranalysis.plugin.image.task.labeller
 
SharedStateFilteredImageOutput(Outputter, ImageLabeller<T>) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
 
SharedStateSegmentInstance<T> - Class in org.anchoranalysis.plugin.image.task.segment
Shared-state for instance segmentation
SharedStateSegmentInstance(ConcurrentModelPool<T>, FeatureTableCalculator<FeatureInputSingleObject>, LabelHeaders, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
 
SharedStateSelectedSlice - Class in org.anchoranalysis.plugin.image.task.slice
 
SharedStateSelectedSlice(Outputter) - Constructor for class org.anchoranalysis.plugin.image.task.slice.SharedStateSelectedSlice
 
Shell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
 
Shell() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
 
shift() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
Increments the slice number by one
shiftBackBy(VoxelsAssigner, ReadableTuple3i) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
Shifts all coordinates BACKWARDS before passing to another VoxelsAssigner.
shiftBackBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Shifts the object-mask by moving its bounding-box backwards (i.e.
shiftBackBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox
Shifts the bounding-box backwards.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
Shifts the bounding-box of each object by adding to it i.e.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Shifts the object-mask by moving its bounding-box forwards (i.e.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox
Shifts the bounding-box forwards.
shiftBy(T, ReadableTuple3i) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
Positionally-shifts an element by a given quantity in the positive direction.
shiftTo(Point3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox
Assigns a new corner-location to the bounding-box.
shiftToOrigin() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
Creates a new object-mask with identical voxels but with the bounding-box beginning at the origin (0,0,0)
shiftToOrigin() - Method in class org.anchoranalysis.spatial.box.BoundingBox
Moves the bounding-box to the origin (0,0,0) but preserves the extent
shiftToZ(int) - Method in class org.anchoranalysis.spatial.box.BoundingBox
Assigns a new z-slice corner-location to the bounding-box
SHORT_OPTION_DEBUG - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_HELP - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_INPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_LOG_ERROR - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_OUTPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_OUTPUT_ENABLE_ALL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_TASK - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
SHORT_OPTION_VERSION - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
 
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
Whether to overwrite the current voxel-value with the constant?
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
 
shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
 
shuffle() - Method in class org.anchoranalysis.core.color.ColorList
 
Shuffle - Class in org.anchoranalysis.bean.shared.color.scheme
Randomizes the order of the colors from existing scheme.
Shuffle<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
Randomly shuffles the order of an input-manager
Shuffle() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Shuffle
 
Shuffle() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Shuffle
 
Shuffle(ColorScheme) - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Shuffle
 
SignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype
 
SignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype
 
SignedVoxelType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
 
SimpleAnnotationDeleter - Class in org.anchoranalysis.annotation.io
Deletes any annotation that is only the file represented at the path
SimpleAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
 
SimpleCopy - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
 
SimpleCopy() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.SimpleCopy
 
SimpleManifestDeserializer - Class in org.anchoranalysis.io.manifest.deserializer
 
SimpleManifestDeserializer() - Constructor for class org.anchoranalysis.io.manifest.deserializer.SimpleManifestDeserializer
 
SimpleName - Class in org.anchoranalysis.feature.io.name
A name with only one part, and is always unique.
SimpleName(String) - Constructor for class org.anchoranalysis.feature.io.name.SimpleName
 
SimpleNameValue<V> - Class in org.anchoranalysis.core.identifier.name
A simple container expressing a name-value pair
SimpleNameValue(String, V) - Constructor for class org.anchoranalysis.core.identifier.name.SimpleNameValue
 
SimpleOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
 
SimpleOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
 
SimpleOverlayWriter - Class in org.anchoranalysis.mpp.io.marks.generator
Converts a configuration to a set of object-masks, using a simple DrawObject for all objects.
SimpleOverlayWriter(DrawObject) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
 
SimplePropertyDefiner<P> - Class in org.anchoranalysis.bean.initializable.property
 
SimplePropertyDefiner(Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
 
SimulatedAnnealing<S,​T,​U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
Finds an optima using a simulated-annealing approach
SimulatedAnnealing() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
 
Single - Class in org.anchoranalysis.image.bean.spatial.arrange
 
Single - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
 
Single() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Single
 
Single() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
 
SingleChannel - Class in org.anchoranalysis.plugin.image.feature.bean.score
A score that is calculated on a single channel only
SingleChannel - Class in org.anchoranalysis.plugin.io.bean.channel.map
For an image with a single channel
SingleChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
 
SingleChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
 
SingleChannel(String) - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
 
SingleColor - Class in org.anchoranalysis.core.color
An index that always uses the same single color
SingleColor(Color) - Constructor for class org.anchoranalysis.core.color.SingleColor
 
SingleColor(RGBColor) - Constructor for class org.anchoranalysis.core.color.SingleColor
 
SingleContainer<T> - Class in org.anchoranalysis.core.index.bounded
 
SingleContainer(boolean) - Constructor for class org.anchoranalysis.core.index.bounded.SingleContainer
 
SingleContainer(T, int, boolean) - Constructor for class org.anchoranalysis.core.index.bounded.SingleContainer
 
SingleFileTypeGenerator<T,​S> - Class in org.anchoranalysis.io.generator
A Generator that eventually writes only a single file to the filesystem.
SingleFileTypeGenerator() - Constructor for class org.anchoranalysis.io.generator.SingleFileTypeGenerator
 
SingleFileTypeGeneratorBridge<S,​T,​V> - Class in org.anchoranalysis.io.generator
Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.
SingleFileTypeGeneratorBridge(SingleFileTypeGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
 
SingleLevelAnd - Class in org.anchoranalysis.io.output.enabled.single
Outputs are enabled if they are contained in both of two SingleLevelOutputEnabled.
SingleLevelAnd(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd
Creates using two SingleLevelOutputEnableds.
SingleLevelBinary - Class in org.anchoranalysis.io.output.enabled.single
Base class for a SingleLevelOutputEnabled that combines two existing such classes.
SingleLevelBinary(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
 
SingleLevelInSet - Class in org.anchoranalysis.io.output.enabled.single
Outputs are enabled if they are contained in a set.
SingleLevelInSet(Set<String>) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet
 
SingleLevelNot - Class in org.anchoranalysis.io.output.enabled.single
The complement of an existing SingleLevelOutputEnabled where disabled outputs are enabled, and vice-versa.
SingleLevelNot(SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelNot
 
SingleLevelOr - Class in org.anchoranalysis.io.output.enabled.single
Outputs are enabled if they are contained in either of two SingleLevelOutputEnabled.
SingleLevelOr(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelOr
Creates using two SingleLevelOutputEnableds.
SingleLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.single
 
SingleMarkProvider - Class in org.anchoranalysis.mpp.bean.provider
Provides (maybe) a single mark
SingleMarkProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.SingleMarkProvider
 
SingleObjectFromChannelFactory - Class in org.anchoranalysis.image.core.object.factory
 
SingleObjectFromPointsFactory - Class in org.anchoranalysis.image.core.object.factory
 
SinglePathStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
 
SinglePathStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
 
singleProcessor(int) - Static method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
Creates a plan for a single-CPU processor
SingleRowPerInput<T extends InputFromManager,​S extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
Base class for exporting features, where features are calculated per-image using a NamedFeatureStore.
SingleRowPerInput(String) - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
 
SingleTableCalculator - Class in org.anchoranalysis.image.feature.session
 
SingleTableCalculator(NamedFeatureStore<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.session.SingleTableCalculator
 
size() - Method in class org.anchoranalysis.core.color.ColorList
 
size() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
size() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
 
size() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
 
size() - Method in class org.anchoranalysis.feature.name.FeatureNameList
 
size() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
 
size() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
size() - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements
Number of scaled-elements.
size() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
size() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
 
size() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
 
size() - Method in class org.anchoranalysis.image.core.stack.NamedStacks
Number of stacks
size() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
 
size() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
 
size() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
 
size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
 
size() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
 
size() - Method in class org.anchoranalysis.math.histogram.Histogram
The number of items in the histogram (maxBin - minBin + 1)
size() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
 
size() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
 
size() - Method in class org.anchoranalysis.mpp.bean.points.updatable.UpdatablePointsContainer
 
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
 
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
size() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
 
size() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
size() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
 
size() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
 
size() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
size() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
size() - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex
 
size() - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
 
size() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
 
size() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
 
size() - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
 
size() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
size() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
 
size() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
 
size() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
 
size() - Method in class org.anchoranalysis.spatial.box.BoundedList
The number of elements
size() - Method in class org.anchoranalysis.spatial.rtree.RTree
 
Size - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
Size() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Size
 
sizeBytes - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
 
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
 
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
 
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
 
sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
sizeCurrentLoad() - Method in class org.anchoranalysis.core.cache.LRUCache
Number of items currently in the cache
sizeCurrentLoad() - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
Number of items currently in the cache
sizeDescriptor(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
Calculates the size of the descriptor will be for a given image, assuming the window is equal to the image-size
SizeExtents - Class in org.anchoranalysis.plugin.io.multifile
Remembers the different sizes among the files
SizeExtents(ParsedFilePathBag) - Constructor for class org.anchoranalysis.plugin.io.multifile.SizeExtents
 
sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
 
sizeFeatures() - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
The number of features that is calculated on each call to calc(), and therefore the size of the ResultsVector returned
sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
 
sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
 
sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
 
sizeFeatures() - Method in class org.anchoranalysis.feature.session.SequentialSession
 
sizeFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
sizeFeatures() - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
 
sizeFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
The number of elements in the first list.
sizeSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
The number of elements in the second list.
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
 
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
 
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
 
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
 
sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
sizeXY - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
 
SizeXY - Class in org.anchoranalysis.image.bean.spatial
 
SizeXY() - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
 
SizeXY(int, int) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
 
SizeXY(Extent) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
Constructor
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
 
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
 
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
 
sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
 
skewness(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics
 
Skewness - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
Skewness() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
 
SkipInit - Annotation Type in org.anchoranalysis.bean.annotation
Indicates that this particular bean-field should be ignored during (recursive) initialisation
slice(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
slice(int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
slice(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
Creates a new Voxels with only particular slice
slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
 
slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
 
slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
 
slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
 
slice(int) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
 
slice(int) - Method in class org.anchoranalysis.image.voxel.Voxels
 
slice(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
SliceAt - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
 
SliceAt() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
 
sliceBuffer(int) - Method in class org.anchoranalysis.image.core.mask.Mask
 
sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
sliceBuffer(int) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
 
sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.Voxels
 
sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
A slice buffer with global coordinates
sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
A slice buffer with global coordinates
SliceBufferIndex<T> - Interface in org.anchoranalysis.image.voxel.factory.sliceindex
Provides voxel-buffers for each z-slice.
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
A slice buffer with local coordinates i.e.
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
A slice buffer with local coordinates i.e.
slices() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
slices() - Method in class org.anchoranalysis.image.voxel.Voxels
 
sliceStatisticsForRegion(VoxelizedMark, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
SliceThresholder - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
 
SliceThresholder(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
 
SliceThresholderMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
 
SliceThresholderMask(boolean, ObjectMask, BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask
 
SliceThresholderWithoutMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
 
SliceThresholderWithoutMask(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask
 
SlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer
Contains the buffer for the current slice, the current slice minus 1, and the current slice plus 1
SlidingBuffer(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
 
Sobel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
3x3 Sobel Filter
Sobel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
 
solveQuadraticEquation(double, double, double) - Static method in class org.anchoranalysis.math.equation.QuadraticEquationSolver
Solves a quadratic equation in form x^2 + b^x + c = 0
sort(Comparator<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
Creates a new feature-list sorted in a particular order.
SortAlphabetically<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
Sorts the input-items in alphabetical order of their input-name.
SortAlphabetically - Class in org.anchoranalysis.plugin.io.bean.provider.file
 
SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
 
SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabetically
 
SortAlphabeticallyWithDirectory - Class in org.anchoranalysis.plugin.io.bean.provider.file
 
SortAlphabeticallyWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabeticallyWithDirectory
 
SortByFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
Creates a new object-collection with objects sorted by a derived feature-value (in ascending order)
SortByFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
 
SortedSetChannel - Class in org.anchoranalysis.plugin.io.multifile
 
SortedSetChannel() - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
 
SortedSetSlice - Class in org.anchoranalysis.plugin.io.multifile
 
SortedSetSlice(String, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
 
sourceVal - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
spatiallySeparate() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
Splits the collection of objects into spatially separate clusters.
SpatiallySeparate<T> - Class in org.anchoranalysis.spatial.rtree
 
SpatiallySeparate(Function<T, BoundingBox>) - Constructor for class org.anchoranalysis.spatial.rtree.SpatiallySeparate
 
SpatialUnits - Class in org.anchoranalysis.image.core.dimensions
Units to describe spatial quantities.
SpatialUnits.UnitSuffix - Enum in org.anchoranalysis.image.core.dimensions
Suffix that describes a particular quantity of units (micron, nano, square microns etc.)
Specific - Class in org.anchoranalysis.plugin.mpp.bean.region
 
Specific() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.Specific
 
SpecificAndRename - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
Selects a specific set of channels from stacks, each identified by a stack-name and channel index
SpecificAndRename() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
 
SpecificAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
A feature based one one-specific principal-axis as identified by image moments.
SpecificAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
 
SpecificDisabled - Class in org.anchoranalysis.io.output.bean.enabled
Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
SpecificDisabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
 
SpecificDisabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
 
SpecificEnabled - Class in org.anchoranalysis.io.output.bean.enabled
Only specific outputs, identified by a textual name, are enabled.
SpecificEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
 
SpecificEnabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
 
SpecificEnergyChannelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
 
SpecificEnergyChannelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
 
Sphere - Class in org.anchoranalysis.mpp.mark.conic
A sphere
Sphere() - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere
 
Sphere(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere
Creates with a radius within particular bounds.
Sphere(Sphere) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere
Copy Constructor
split(Path) - Method in class org.anchoranalysis.bean.shared.path.RootPath
It splits the *root* portion of the path from the remainder
split(Path, String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
Given a path, it splits the *root* portion of the path from the remainder, trying a root identified by the rootName and debugMode (and if this fails, also trying with debugMode==false)
SplitByObjects - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
 
SplitByObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
 
SplitContourAtSaddlePoints - Class in org.anchoranalysis.plugin.points.bean.provider.object
Splits a 2D contour represented by an object-mask into several contours, splitting at "turn" points.
SplitContourAtSaddlePoints() - Constructor for class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
 
SplitContourSmoothingSpline - Class in org.anchoranalysis.plugin.points.bean.contour
 
SplitIntoSquares - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
SplitIntoSquares() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
 
SplitPath - Class in org.anchoranalysis.core.system.path
A path that has been split into two components: a root and a remainder.
SplitPath(Path, Path) - Constructor for class org.anchoranalysis.core.system.path.SplitPath
 
SQUARE_MICRO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
 
SQUARE_NANO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
 
stack() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
 
stack(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
 
Stack - Class in org.anchoranalysis.image.core.stack
One ore more single-channel images that all have the same dimensions.
Stack() - Constructor for class org.anchoranalysis.image.core.stack.Stack
 
Stack(Stream<Channel>) - Constructor for class org.anchoranalysis.image.core.stack.Stack
 
Stack(Channel) - Constructor for class org.anchoranalysis.image.core.stack.Stack
 
Stack(Channel...) - Constructor for class org.anchoranalysis.image.core.stack.Stack
 
Stack(Dimensions, ChannelFactorySingleType, int) - Constructor for class org.anchoranalysis.image.core.stack.Stack
 
StackIdentifiers - Class in org.anchoranalysis.image.experiment.identifiers
 
StackNotUniformSized - Class in org.anchoranalysis.image.core.stack
 
StackNotUniformSized() - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
StackNotUniformSized(Stream<Channel>) - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
StackNotUniformSized(Channel) - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized
 
StackProvider - Class in org.anchoranalysis.image.bean.provider.stack
 
StackProvider() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProvider
 
StackProviderUnary - Class in org.anchoranalysis.image.bean.provider.stack
 
StackProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
 
stacks() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
 
stacks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
 
Stacks - Class in org.anchoranalysis.plugin.io.bean.input.stack
Each file gives either: * a single stack * a time-series of stacks
Stacks() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
 
Stacks(InputManager<FileInput>) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
 
STACKS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories
Where stacks are typically placed in a define-experiment output
stackTrace() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
Prints a stack trace of the current exception to a string
StackWithMap - Class in org.anchoranalysis.mpp.io.input
Combines a Stack with a map of other stacks
StackWithMap(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.StackWithMap
 
standardDeviation() - Method in class org.anchoranalysis.math.histogram.Histogram
 
StandardDeviation - Class in org.anchoranalysis.feature.bean.results
The standard-deviation of the results from a particular feature.
StandardDeviation() - Constructor for class org.anchoranalysis.feature.bean.results.StandardDeviation
 
start() - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
 
start() - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
 
start() - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
 
start() - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
 
start() - Method in interface org.anchoranalysis.experiment.log.StatefulMessageLogger
 
start() - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
 
start() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
 
start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
 
start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
 
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
 
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
 
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
 
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
 
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
 
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
 
start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
 
start(FeatureInitParams, SharedFeatureMulti, Logger) - Method in class org.anchoranalysis.feature.session.SequentialSession
Starts the session
start(EnergyStack) - Method in class org.anchoranalysis.mpp.feature.bean.mark.CheckMark
start(EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
 
start(EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
 
start(ImageInitParams, Optional<EnergyStack>, Logger) - Method in interface org.anchoranalysis.image.feature.session.FeatureTableCalculator
Initializes a feature store that has the same structure as that previously created by createFeatures() from the same object
start(ImageInitParams, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
 
start(ImageInitParams, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
 
start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
 
start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects
Initializes a batch to create thumbnails.
start(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
 
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
Derives a list of inputs from an object-collection
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
 
startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
 
startSeries(NoSharedState, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
 
startSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
 
startSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
 
startSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
Starts processing of a series.
StatefulMessageLogger - Interface in org.anchoranalysis.experiment.log
A MessageLogger that can be started and stopped, and is aware this state.
StatefulNullMessageLogger - Class in org.anchoranalysis.experiment.bean.log
Does nothing (i.e.
StatefulNullMessageLogger() - Constructor for class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
 
stateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
 
stateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
 
stateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
StateReporter<T,​S> - Class in org.anchoranalysis.mpp.segment.bean.optimization
Converts the optimization state to a form that the reporter needs
StateReporter() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.StateReporter
 
StateReporterIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
Assumes the state is reported without any transformation
StateReporterIdentity() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterIdentity
 
StateReporterToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
Assumes we are interested in VoxelizedMarksWithEnergy as reporting type, and our optimization-state is in the form ToPixelized<T>
StateReporterToPixelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
 
StateReporterTransformer<T,​S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
 
StateReporterTransformer() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
 
stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridge
 
stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeIdentity
 
stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
 
stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
 
StateTransformer<W,​X> - Interface in org.anchoranalysis.mpp.segment.transformer
 
StateTransformerBean<S,​T> - Class in org.anchoranalysis.mpp.segment.transformer
Transforms one type into another
StateTransformerBean() - Constructor for class org.anchoranalysis.mpp.segment.transformer.StateTransformerBean
 
StaticFilePath - Class in org.anchoranalysis.plugin.io.bean.filepath
 
StaticFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
 
StatisticalScoreBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.score
Calculates a score based upon the statistical mean and std-deviation.
StatisticalScoreBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
 
StatisticForFeature - Class in org.anchoranalysis.feature.bean.results
Base class for calculating a statistic across all results in a ResultsVectorList for a particular feature.
StatisticForFeature() - Constructor for class org.anchoranalysis.feature.bean.results.StatisticForFeature
 
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Mean
 
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Quantile
 
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.StandardDeviation
 
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
 
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Sum
 
statisticsFor(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
 
statisticsForAllSlices(int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
 
statisticsForAllSlices(VoxelizedMark, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
statisticsForAllSlicesMaskSlice(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
 
stdDev() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
StdDev - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
StdDev() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StdDev
 
Steepest - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
 
Steepest(SlidingBuffer<?>, WatershedEncoding, boolean, boolean, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest
 
steepestDescent(Point3i, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest
 
StoreSupplier<T> - Interface in org.anchoranalysis.core.identifier.provider.store
Supplier of an object for a store
strategyForGrandchild() - Method in class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
 
strategyForGrandchild() - Method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
 
strategyForGrandchild() - Method in interface org.anchoranalysis.feature.session.strategy.child.FindChildStrategy
What strategy to use for children-of-children?
stream() - Method in class org.anchoranalysis.core.functional.StreamableCollection
 
stream() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
 
stream() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
 
stream() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
Provides various functional-programming operations on the object-collection
stream() - Method in class org.anchoranalysis.spatial.box.BoundedList
A stream of elements in the list.
StreamableCollection<T> - Class in org.anchoranalysis.core.functional
As a stream can only be used once, this data-structure allows for repeatedly getting streams from a collection
StreamableCollection(Collection<T>) - Constructor for class org.anchoranalysis.core.functional.StreamableCollection
Create for a particular collection
StreamableCollection(Supplier<Stream<T>>) - Constructor for class org.anchoranalysis.core.functional.StreamableCollection
 
streamOverZ() - Method in class org.anchoranalysis.spatial.Extent
Streams over the range of z values
streamStandardJava() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
A stream of object-masks as per Java's standard collections interface
StringBeanCollection - Interface in org.anchoranalysis.bean
A bean that provides a collection of Strings.
StringGenerator - Class in org.anchoranalysis.io.generator.text
 
StringGenerator() - Constructor for class org.anchoranalysis.io.generator.text.StringGenerator
 
StringList - Class in org.anchoranalysis.bean
A list of strings (order is defined).
StringList() - Constructor for class org.anchoranalysis.bean.StringList
 
StringListFactory - Class in org.anchoranalysis.bean.xml.factory
Creates a StringList from a XML element.
StringListFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.StringListFactory
 
StringMap - Class in org.anchoranalysis.bean.shared
 
StringMap() - Constructor for class org.anchoranalysis.bean.shared.StringMap
 
StringMapItem - Class in org.anchoranalysis.bean.shared
A simple mapping from one string (source) to another (target)
StringMapItem() - Constructor for class org.anchoranalysis.bean.shared.StringMapItem
 
stringRepresentationForElement(int) - Method in interface org.anchoranalysis.io.manifest.sequencetype.IncompleteElementRange
Returns the typed-index corresponding to the integer-index.
StringSet - Class in org.anchoranalysis.bean
A set of strings.
StringSet() - Constructor for class org.anchoranalysis.bean.StringSet
 
StringSet(String...) - Constructor for class org.anchoranalysis.bean.StringSet
 
StringSetFactory - Class in org.anchoranalysis.bean.xml.factory
Creates a StringSet from a XML element.
StringSetFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.StringSetFactory
 
StringSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
 
StringSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
 
StringSuffixOutputNameStyle(String, Optional<String>) - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
 
StringsWithoutOrder - Class in org.anchoranalysis.io.manifest.sequencetype
A sequence of strings that has no order.
StringsWithoutOrder() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
 
strMarks() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
 
strPos() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
 
subdirectories() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
The MutableDirectory in the manifest for any subdirectories.
subdirectory(String, ManifestDirectoryDescription, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
Creates a new context that writes instead to a subdirectory.
Subdirectory - Class in org.anchoranalysis.io.manifest.directory
A SubdirectoryBase entry in the manifest for a subdirectory.
Subdirectory() - Constructor for class org.anchoranalysis.io.manifest.directory.Subdirectory
 
Subdirectory(Path) - Constructor for class org.anchoranalysis.io.manifest.directory.Subdirectory
 
SubdirectoryBase - Class in org.anchoranalysis.io.manifest.directory
 
SubdirectoryBase() - Constructor for class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
 
SubdirectoryBase(Path) - Constructor for class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
 
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
An optional subdirectory where the group outputs are placed.
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
 
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
 
subList(int, int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
SUBMARK_CORE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
 
SUBMARK_CORE_INNER - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
 
SUBMARK_INSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
 
SUBMARK_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
 
SUBMARK_SHELL - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
 
SUBMARK_SHELL_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
 
SubmittedJob - Class in org.anchoranalysis.experiment.task.processor
 
SubmittedJob(JobDescription, JobState) - Constructor for class org.anchoranalysis.experiment.task.processor.SubmittedJob
 
subset(StringSet) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
Creates a new collection containing only items whose keys exist in a particular set
subsetCompatibleWith(Class<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
Extracts the subset of inputs that are compatible with a particular input-type
subsetWhereBBoxIntersects(Dimensions, int, List<BoundingBox>) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
 
subsetWhereBBoxIntersects(Dimensions, DrawOverlay, List<BoundingBox>) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
subtract(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
subtract(VarianceCalculator) - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
 
subtract(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
 
subtract(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
subtract(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
subtractBackground(Channel, int, boolean) - Static method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
 
subtractFrom(int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic
Subtracts all current voxel-values from a constant-value
SubtractFrom<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
SubtractFrom() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
 
SubtractFromConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
SubtractFromConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
 
subtractFromMaxValue() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
SubtractMean - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
SubtractMean() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
 
SubtractReducedFromMerged - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
Calculates merged - reduce(first,second) for a FeatureInputPairObjects
SubtractReducedFromMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
 
SubtractSecondFromFirst - Class in org.anchoranalysis.image.feature.bean.object.pair
Subtract second-object from first-object in a pair
SubtractSecondFromFirst() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst
 
SubtractTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
 
SubtractTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractTwoChannels
 
suffixStringForMeters(SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
A string that describes the suffix for meters.
sum() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
 
sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
 
sum() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
Sum<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
 
Sum - Class in org.anchoranalysis.feature.bean.results
The sum of the results from a particular feature.
Sum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
Sum() - Constructor for class org.anchoranalysis.feature.bean.operator.Sum
 
Sum() - Constructor for class org.anchoranalysis.feature.bean.results.Sum
 
Sum() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
 
Sum(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.Sum
 
sumBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
 
summarize() - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
This summarize() option just looks for the most deep exception that can be 'combined' and takes its message
summarize() - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
 
summarize() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
 
summarize() - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
 
SummarizeBase<T extends InputFromManager,​S> - Class in org.anchoranalysis.plugin.io.bean.task
 
SummarizeBase() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
 
summarizeDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
A comma-separated string of all output-names that were not enabled.
summarizeEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
A comma-separated string of all output-names that were enabled.
summarizeIgnoreIdenticalFilePath(Path) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
If there is no nested-set of combinable exceptions, and the filenameDscr related to this current exception, is identical as the passed parameter, then we simply ignore the LocalisedBean and promote its getCause()
SummarizeInputs<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.task
 
SummarizeInputs() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
 
summarizeMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
Summarizer<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
Summarizes a set of elements by outputting a descriptive string
Summarizer() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer
 
SummarizerAggregate<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
Collects summary data about a set of input files that will eventually be outputted to the user
SummarizerAggregate() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
 
SummarizerCount<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
A count of the number of inputs.
SummarizerCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
 
SummarizerInputFromManager<T extends InputFromManager,​S> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
Extracts a particular item from an InputManager for summarization downstream
SummarizerInputFromManager() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
 
SummarizerListMultiline<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
Creates a string where each line is an element (the string representation thereof)
SummarizerListMultiline() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
 
SummarizerNamedChannels<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
Summarzes NamedChannelsInput in different ways
SummarizerNamedChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
 
SummarizerNamedChannelsSimple<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
A simple summerizer where there's one summary-item per image (series are ignored!)
SummarizerNamedChannelsSimple() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannelsSimple
 
SummarizerSplitMoreThan<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
Multiplexes between two summarizers depending on the total number of count
SummarizerSplitMoreThan() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
 
SummaryException - Exception in org.anchoranalysis.core.exception.combinable
A special kind of exception that represents a summary of an existing set of exceptions
SummaryException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.combinable.SummaryException
 
summaryStr() - Method in class org.anchoranalysis.spatial.Contour
 
sumNonZero() - Method in class org.anchoranalysis.math.histogram.Histogram
 
sumOfSquares() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
 
sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
 
sumOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
 
SupportsTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer
Base class for ImageJRasterWriter that does support writing time-series as a stack.
SupportsTimeSeries() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.SupportsTimeSeries
 
suppressedLogErrorReporter() - Static method in class org.anchoranalysis.test.LoggingFixture
A Logger that doesn't output anything
suppressedLogReporter() - Static method in class org.anchoranalysis.test.LoggingFixture
A MessageLogger that doesn't output anything
SuppressNonMaxima<T> - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
Applies a segmentation procedure followed by non-maxima suppression.
SuppressNonMaxima() - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
 
SuppressNonMaxima(SegmentStackIntoObjectsPooled<T>) - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
Creates with a particular segmentation algorithm as an input.
SuppressNonMaxima(SegmentStackIntoObjectsPooled<T>, ReduceElements<ObjectMask>) - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
 
SurfaceNumberVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
The number of voxel-faces along the surface (the faces of each voxel that touch outside)
SurfaceNumberVoxelFaces() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelFaces
 
SurfaceNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
The number of voxels on the surface (all voxels on the exterior of the object)
SurfaceNumberVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
 
SurfaceNumberVoxelsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
 
SurfaceNumberVoxelsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
 
SurfaceSizeMaskNonZero - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
 
SurfaceSizeMaskNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
 
SwitchChannelTime - Class in org.anchoranalysis.io.bioformats.bean.options
Treats the channel index as if it's time, and vice versa
SwitchChannelTime() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
 
SwitchDetailedLogging - Class in org.anchoranalysis.experiment.bean.log
Switches between two log-reporters depending on whether detailed logging is switched on or not
SwitchDetailedLogging() - Constructor for class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
 

T

TableItemArrangement<T> - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
 
TableItemArrangement(TableItemArrangement.TableCreator<T>, int, int) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
 
TableItemArrangement.TableCreator<T> - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
 
TableItemException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
 
TableItemException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemException
 
TableItemException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemException
 
tail() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
 
Task<T extends InputFromManager,​S> - Class in org.anchoranalysis.experiment.bean.task
A task which performs some kind of processing on a specific input-object
Task() - Constructor for class org.anchoranalysis.experiment.bean.task.Task
 
TaskFactory - Class in org.anchoranalysis.launcher.executor.selectparam.task
A factory that creates SelectParam<Optional<Path>> as required for tasks.
TaskStatistics - Class in org.anchoranalysis.experiment.task
Maintains statistics on the execution of a task (considering jobs in aggregate)
TaskStatistics(long, RunningSum, RunningSum) - Constructor for class org.anchoranalysis.experiment.task.TaskStatistics
 
TaskWithoutSharedState<T extends InputFromManager> - Class in org.anchoranalysis.experiment.bean.task
A particular type of task that doesn't share-state between running jobs
TaskWithoutSharedState() - Constructor for class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
 
TerminationCondition - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination
A test on whether to terminate the optimization or not
TerminationCondition() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationCondition
 
TerminationConditionListOr - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination
 
TerminationConditionListOr() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
 
TerminationConditionListOr(TerminationCondition, TerminationCondition) - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
 
test(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes
Do the combination of two arguments fulfill the predicate?
test(Point3i, T, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.buffer.PredicateBufferBinary
Tests a voxel location in two buffers
test(T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedPredicate
Applies a predicate like with Predicate.test(T).
TestDataInitException - Exception in org.anchoranalysis.test
An exception thrown when test-data cannot be loaded
TestDataInitException(String) - Constructor for exception org.anchoranalysis.test.TestDataInitException
 
TestDataInitException(Throwable) - Constructor for exception org.anchoranalysis.test.TestDataInitException
 
TestDataLoadException - Exception in org.anchoranalysis.test
An exception thrown when test-data cannot be loaded
TestDataLoadException(String) - Constructor for exception org.anchoranalysis.test.TestDataLoadException
 
TestDataLoadException(Throwable) - Constructor for exception org.anchoranalysis.test.TestDataLoadException
 
TestLoader - Class in org.anchoranalysis.test
Loads test data, which is found at some location on the filesystem
TestLoaderMPP - Class in org.anchoranalysis.test.experiment
 
TestLoaderMPP(TestLoader) - Constructor for class org.anchoranalysis.test.experiment.TestLoaderMPP
 
testManifestExperiment(String) - Method in class org.anchoranalysis.test.TestLoader
 
textColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
textColor() - Method in class org.anchoranalysis.core.color.RGBColor
 
TextFile - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
TextFile() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
 
TextFileAsIntegerFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
 
TextFileAsIntegerFromManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromManifest
 
TextFileAsIntegerFromPath - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
 
TextFileAsIntegerFromPath() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromPath
 
TextFileMarksReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
TextFileMarksReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
 
TextFileMessageLogger - Class in org.anchoranalysis.experiment.log
Logs messages to a text-file.
TextFileMessageLogger(String, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.TextFileMessageLogger
Constructs a logger that (always) writes messages to a text-file with a specific path.
TextFileMessageLogger(String, OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.TextFileMessageLogger
Constructs a logger that (maybe) writes messages to a text-file, with a path based upon an output name applied to a OutputterChecked.
TextFileOutput - Class in org.anchoranalysis.io.generator.text
Utility for writing to a text-file at a particular path, but only if it is enabled.
TextFileOutput(String) - Constructor for class org.anchoranalysis.io.generator.text.TextFileOutput
 
TextFileOutputter - Class in org.anchoranalysis.io.generator.text
Maybe creates a TextFileOutput based upon settings in a OutputterChecked.
TextFileReader - Class in org.anchoranalysis.io.manifest.file
 
TextureScore - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
From Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei
TextureScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
 
ThreeChannels - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
 
ThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
 
ThreeColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
ThreeColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
 
ThreeWayBranchXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
Takes the XY-resolution determined by stackReaderInput.
ThreeWayBranchXYResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
 
threshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
threshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold
The threshold-value
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
 
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
 
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
 
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
 
threshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
 
threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
 
threshold(VoxelsWrapper) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder
Like Thresholder.threshold(VoxelsWrapper) but using default binary-values.
threshold(VoxelsWrapper, BinaryValuesByte) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder
Like Thresholder.threshold(VoxelsWrapper, BinaryValuesByte, Optional, Optional) applying the thresholding to the entire set of voxels.
threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder
Thresholds voxels (across a range of values) so that they have only binary range (i.e.
threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
 
threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
 
threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
 
threshold(RelationToValue, double) - Method in class org.anchoranalysis.math.histogram.Histogram
 
Threshold - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment
Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible.
Threshold() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
 
ThresholdAgainstChannel - Class in org.anchoranalysis.plugin.image.bean.segment.binary
Thresholds each voxels by comparing against another channel that has per-voxel thresholds
ThresholdAgainstChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
 
ThresholdConfidence - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
Combines object-masks by projecting the maximum confidence-level for each voxel and thresholding.
ThresholdConfidence() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
 
ThresholdConfidence(double) - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
Creates with a minimum-confidence level.
Thresholded - Class in org.anchoranalysis.plugin.mpp.bean.region
 
Thresholded() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
 
ThresholdedFeature - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
ThresholdedFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
 
ThresholdedVolume - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
ThresholdedVolume() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
 
Thresholder - Class in org.anchoranalysis.image.bean.threshold
Thresholds a voxels to create a binary-voxels
Thresholder() - Constructor for class org.anchoranalysis.image.bean.threshold.Thresholder
 
ThresholderAutoIJ - Class in org.anchoranalysis.plugin.fiji.bean.threshold
 
ThresholderAutoIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
 
ThresholderGlobal - Class in org.anchoranalysis.image.bean.threshold
Performs global thresholding.
ThresholderGlobal() - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
 
ThresholderGlobal(CalculateLevel) - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
 
ThresholderSimpleFillHoles2D - Class in org.anchoranalysis.plugin.imagej.bean.threshold
 
ThresholderSimpleFillHoles2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
 
ThresholderSimpleFillHoles2D(int) - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
 
thresholdForLevel(Voxels<UnsignedByteBuffer>, int, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder
 
thresholdForLevel(VoxelsWrapper, int, BinaryValuesByte, Optional<ObjectMask>, boolean) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder
 
ThresholdHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
Thresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded version
ThresholdHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
 
ThumbnailBatch<T> - Interface in org.anchoranalysis.plugin.image.thumbnail
Creates thumbnails for a particular batch of objects that can be calibrated to have similar properties (identical scale etc.)
thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
 
thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack
Creates a thumbnail for a stack
thumbnailFor(T) - Method in interface org.anchoranalysis.plugin.image.thumbnail.ThumbnailBatch
Creates a thumbnail for an element in the batch
ThumbnailFromObjects - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object
Creates a thumbnail of one or more objects on a stack by drawing the outline of the objects
ThumbnailFromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects
 
ThumbnailFromStack - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack
Creates a thumbnail from a stack
ThumbnailFromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack
 
Tiff - Class in org.anchoranalysis.io.imagej.bean.stack.writer
Writes a TIFF image using ImageJ.
Tiff - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
Writes a stack to the filesystem as a TIFF using the Bioformats library.
Tiff() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
 
Tiff() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
 
TiffTimeSeries - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
TiffTimeSeries() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
 
Tile - Class in org.anchoranalysis.image.bean.spatial.arrange
 
Tile() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Tile
 
TimeSequence - Class in org.anchoranalysis.image.core.stack
 
TimeSequence() - Constructor for class org.anchoranalysis.image.core.stack.TimeSequence
 
TimeSequence(Stack) - Constructor for class org.anchoranalysis.image.core.stack.TimeSequence
 
title() - Method in class org.anchoranalysis.io.output.bean.ReportFeature
 
title() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
 
title() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
 
title() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
 
title() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
 
title() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
 
toAll() - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
Assigns to all the voxels
toArray() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
toArray(T[]) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
 
toAWTColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
 
toAWTColor() - Method in class org.anchoranalysis.core.color.RGBColor
 
toBox(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
Assigns to only voxels inside a bounding-box
ToByte - Class in org.anchoranalysis.image.voxel.convert
Base class for conversion to unsigned 8-bit.
ToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert
 
ToByte() - Constructor for class org.anchoranalysis.image.voxel.convert.ToByte
 
ToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
 
ToByteNoScaling - Class in org.anchoranalysis.image.voxel.convert
Converts voxel buffers to a unsigned 8-bit buffer without scaling any values.
ToByteNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
 
ToByteScaleByMaxValue - Class in org.anchoranalysis.image.voxel.convert
Converts voxel buffers to a unsigned 8-bit buffer linearly scaling against the maximum constant value.
ToByteScaleByMaxValue(int) - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
 
ToByteScaleByMinMaxValue - Class in org.anchoranalysis.image.voxel.convert
Converts voxel buffers to a unsigned 8-bit buffer scaling against a the minimum and maximum constant.
ToByteScaleByMinMaxValue(int, int) - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
 
ToByteScaleByType - Class in org.anchoranalysis.image.voxel.convert
Converts voxel buffers to a UnsignedByteBuffer scaling against the maximum value in each buffer.
ToByteScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
 
ToByteUpperLowerQuantileIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.convert.histogram
 
ToByteUpperLowerQuantileIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
 
toChannel(ImagePlus, Optional<Resolution>) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertFromImagePlus
Converts an ImagePlus to a Channel.
toCommandLineException() - Method in exception org.anchoranalysis.launcher.executor.selectparam.path.InvalidPathArgumentException
 
ToConsole - Class in org.anchoranalysis.experiment.bean.log
Logs messages to the console.
ToConsole() - Constructor for class org.anchoranalysis.experiment.bean.log.ToConsole
 
toEitherTwoObjects(ObjectMask, ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
Sets voxels to a value if the position is ON in either of two masks
toExtent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
 
toFloat() - Method in class org.anchoranalysis.spatial.point.Point2d
 
ToFloat - Class in org.anchoranalysis.image.core.channel.convert
 
ToFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
 
ToFloat() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToFloat
 
ToFloat() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
 
ToFloatNoScaling - Class in org.anchoranalysis.image.voxel.convert
Converts voxel buffers to a FloatBuffer without scaling any values.
ToFloatNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
 
ToInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint
 
ToInt() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toint.ToInt
 
ToMultiple - Class in org.anchoranalysis.experiment.bean.log
Rather than logging to one location, logs to multiple locations (from a list).
ToMultiple() - Constructor for class org.anchoranalysis.experiment.bean.log.ToMultiple
 
ToMultiple(LoggingDestination, LoggingDestination) - Constructor for class org.anchoranalysis.experiment.bean.log.ToMultiple
Constructs a logger to two locations
toObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
Sets voxels in a box to a particular value if they match an object-mask
toObject(ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
Sets voxels in a box to a particular value if they match a object-mask (but only a part of the object-mask)
toObjectIf(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
Sets voxels in a box to a particular value if they match an object-mask and a voxel matches a predicate
toObjectWhile(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
Sets voxels in a box to a particular value if they match an object-mask and each voxel matches a predicate
toPhysicalArea(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts an area from square voxels to square meters.
toPhysicalArea(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts an area from square voxels to physical units.
toPhysicalDistance(double, DirectionVector) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts a distance from voxels to meters.
toPhysicalDistance(double, DirectionVector, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts a distance from voxels to physical units.
toPhysicalVolume(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts a volume from cubic voxels to cubic meters.
toPhysicalVolume(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
Converts a volume from cubic voxels to physical units.
ToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
Before and after state, when a src is coverted in a VoxelizedMarksWithEnergy
ToPixelized(T, VoxelizedMarksWithEnergy) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
 
ToPixelizedExtracter<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
 
ToPixelizedExtracter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.ToPixelizedExtracter
 
toSet() - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
Converts to a HashSet (newly-created).
ToShortNoScaling - Class in org.anchoranalysis.image.voxel.convert
Converts voxel buffers to a unsigned 16-bit buffer without scaling any values.
ToShortNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
 
ToShortScaleByType - Class in org.anchoranalysis.image.voxel.convert
Converts voxel buffers to a unsigned 16-bit buffer, scaling against the maximum value in each data-type.
ToShortScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
 
toStack(Mat) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertFromMat
 
toString() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
 
toString() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
 
toString() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
 
toString() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
 
toString() - Method in class org.anchoranalysis.bean.AnchorBean
By default, we use AnchorBean.describeBean() as the string representation of the bean.
toString() - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
 
toString() - Method in class org.anchoranalysis.bean.NamedBean
 
toString() - Method in class org.anchoranalysis.bean.shared.regex.RegExList
 
toString() - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
 
toString() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
 
toString() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
 
toString() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
 
toString() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
 
toString() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
 
toString() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
 
toString() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
toString() - Method in class org.anchoranalysis.core.color.RGBColor
 
toString() - Method in exception org.anchoranalysis.core.exception.AnchorRuntimeException
 
toString() - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
 
toString() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
 
toString() - Method in class org.anchoranalysis.core.graph.TypedEdge
 
toString() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
 
toString() - Method in class org.anchoranalysis.core.log.CommonContext
 
toString() - Method in class org.anchoranalysis.core.system.path.SplitPath
 
toString() - Method in class org.anchoranalysis.core.value.TypedValue
 
toString() - Method in class org.anchoranalysis.experiment.task.InputTypesExpected
 
toString() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
 
toString() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
 
toString() - Method in class org.anchoranalysis.feature.bean.Feature
 
toString() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
 
toString() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
 
toString() - Method in class org.anchoranalysis.feature.energy.EnergyTotal
 
toString() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
 
toString() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
 
toString() - Method in class org.anchoranalysis.feature.io.name.CombinedName
 
toString() - Method in interface org.anchoranalysis.feature.io.name.MultiName
The full name, including both directory and file part, as a string.
toString() - Method in class org.anchoranalysis.feature.io.name.SimpleName
 
toString() - Method in class org.anchoranalysis.feature.name.FeatureNameList
 
toString() - Method in class org.anchoranalysis.feature.results.ResultsVector
 
toString() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
 
toString() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
 
toString() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
 
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
 
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
 
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
 
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
 
toString() - Method in class org.anchoranalysis.image.core.channel.Channel
Display a histogram of voxel-intensities as the string-representation
toString() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
toString() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
toString() - Method in class org.anchoranalysis.image.core.mask.Mask
 
toString() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
 
toString() - Method in class org.anchoranalysis.image.core.object.MatchedObject
 
toString() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
 
toString() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
toString() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
 
toString() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
 
toString() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
 
toString() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
 
toString() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
 
toString() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
 
toString() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
 
toString() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
 
toString() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
 
toString() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
 
toString() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
 
toString() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
 
toString() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
 
toString() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
 
toString() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
 
toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
Default string representation of the collection, one line with each object described by its center-of-gravity
toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
A string representation of the object-mask showing: the center-of-gravity the number of "ON" voxels on the object
toString() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
 
toString() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
 
toString() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
 
toString() - Method in class org.anchoranalysis.io.manifest.file.FileType
 
toString() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
 
toString() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
 
toString() - Method in class org.anchoranalysis.io.output.outputter.Outputter
 
toString() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
 
toString() - Method in class org.anchoranalysis.launcher.config.HelpConfig
 
toString() - Method in class org.anchoranalysis.math.histogram.Histogram
 
toString() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
 
toString() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
 
toString() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
 
toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
 
toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
 
toString() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
 
toString() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
 
toString() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
toString() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
toString() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
 
toString() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
 
toString() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
 
toString() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
 
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
 
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
 
toString() - Method in class org.anchoranalysis.mpp.mark.Mark
String representation of the mark
toString() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
 
toString() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
toString() - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
toString() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
toString() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
toString() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
toString() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
 
toString() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
 
toString() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
 
toString() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
 
toString() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
 
toString() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
 
toString() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
 
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
 
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
 
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
 
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
 
toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
 
toString() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
toString() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
 
toString() - Method in class org.anchoranalysis.plot.AxisLimits
 
toString() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
 
toString() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
 
toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
 
toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
 
toString() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
 
toString() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
 
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
 
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
 
toString() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
 
toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
 
toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
 
toString() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
toString() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
toString() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
 
toString() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
 
toString() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
 
toString() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
 
toString() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
 
toString() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
 
toString() - Method in class org.anchoranalysis.spatial.box.BoundingBox
 
toString() - Method in class org.anchoranalysis.spatial.Extent
 
toString() - Method in class org.anchoranalysis.spatial.point.Point2d
 
toString() - Method in class org.anchoranalysis.spatial.point.Point2f
 
toString() - Method in class org.anchoranalysis.spatial.point.Point2i
 
toString() - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
toString() - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
toString() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
toString() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
toString() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
 
toString(boolean, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
A string representation of all objects in the collection using their center of gravities (and optionally indices)
toStringUnixStyle(String) - Static method in class org.anchoranalysis.core.system.path.FilePathToUnixStyleConverter
Converts a path to a string using Unix-style separators (forward-slashes)
toStringUnixStyle(Path) - Static method in class org.anchoranalysis.core.system.path.FilePathToUnixStyleConverter
Converts a path to a string using Unix-style separators (forward-slashes)
total() - Method in class org.anchoranalysis.feature.results.ResultsVector
 
totalAll(MemoCollection, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
 
TotalCount - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
TotalCount() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
 
totalIndividual(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
 
totalMinusGPUs() - Method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
 
totalNumber() - Method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
 
totalNumberSlices() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
The total number of z-slices across all frames, channels
totalNumberVoxelPositions() - Method in class org.anchoranalysis.spatial.Extent
Calculates the total number of pixel positions needed to represent this bounding box as a pixel array This is not the same as volume, both the start and end pixel are included
ToTextFile - Class in org.anchoranalysis.experiment.bean.log
Logs to a text-file created in the output-directory under a particular name.
ToTextFile() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFile
 
ToTextFileBase - Class in org.anchoranalysis.experiment.bean.log
 
ToTextFileBase() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFileBase
 
ToTextFileOnlyIfFailure - Class in org.anchoranalysis.experiment.bean.log
Logs to a text file like with ToTextFile but the log is ONLY written if a failure occurs in the experiment.
ToTextFileOnlyIfFailure() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFileOnlyIfFailure
 
ToThePowerOfConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
 
ToThePowerOfConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
 
TouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
Base class for features that calculate touching with a dilated bounding box intersection
TouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
 
ToUnsignedByte - Class in org.anchoranalysis.image.core.channel.convert
Converts from other data types to UnsignedByteBuffer (unsigned 8-bit) without scaling.
ToUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
 
ToUnsignedByte() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByte
 
ToUnsignedByte() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
 
ToUnsignedByte(VoxelsConverter<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByte
 
ToUnsignedByteScaleByMinMaxValue - Class in org.anchoranalysis.image.core.channel.convert
Converts from other data types to UnsignedByteBuffer (unsigned 8-bit) scaling from the range of the source data-type.
ToUnsignedByteScaleByMinMaxValue(int, int) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByteScaleByMinMaxValue
 
ToUnsignedShort - Class in org.anchoranalysis.image.core.channel.convert
 
ToUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort
 
ToUnsignedShort() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedShort
 
ToUnsignedShort(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
 
ToUnsignedShort(VoxelsConverter<UnsignedShortBuffer>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedShort
 
toVoxel(int, int, int) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
Assigns one particular voxel
toVoxel(Point3i) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
Assigns one particular voxel
toVoxels(ImagePlus) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertFromImagePlus
Converts an ImagePlus to a VoxelsWrapper.
transferFrom(int, VoxelBuffer<T>, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
 
transferFromConvert(int, VoxelBuffer<?>, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
 
transferSlice(int, VoxelsWrapper, int, boolean) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
transferSlicesResizeXY(VoxelsWrapper, VoxelsWrapper, Interpolator) - Static method in class org.anchoranalysis.image.voxel.interpolator.InterpolateUtilities
 
transferValue(int, int) - Method in class org.anchoranalysis.math.histogram.Histogram
 
transform(Collection<File>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
 
transform(Collection<File>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
 
transform(Collection<File>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabeticallyWithDirectory
 
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
 
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Limit
 
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RandomOrder
 
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
 
transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabetically
 
transform(Optional<W>, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformMapOptional
 
transform(Assignment) - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
 
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
Transform an existing ColorList.
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
 
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
 
transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Shuffle
 
transform(VoxelizedMarksWithEnergy, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
 
transform(ColoredMarksWithDisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
 
transform(MarkCollection) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
 
transform(MarkCollection, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
 
transform(MarkCollection, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.AddEnergy
 
transform(StateTransformer<T, S>, TransformationContext) - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
 
transform(DualVoxelizedMarks, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveDestinationFromDual
 
transform(DualVoxelizedMarks, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveSourceFromDual
 
transform(MarksFromPartition, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartition
 
transform(MarksFromPartition, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
 
transform(ToPixelized<T>, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveDestinationFromVoxelized
 
transform(ToPixelized<T>, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveSourceFromVoxelized
 
transform(S, TransformationContext) - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
 
transform(T) - Method in class org.anchoranalysis.io.generator.OneStageGenerator
 
transform(T) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
 
transform(T) - Method in interface org.anchoranalysis.io.generator.TransformingGenerator
Applies any necessary preprocessing to create an element suitable for writing to the filesystem.
transform(T) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
 
transform(T, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
 
transform(W, TransformationContext) - Method in interface org.anchoranalysis.mpp.segment.transformer.StateTransformer
 
TransformationAssignMode<S,​T,​U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
Applies a transformation to the kernel-type U to calculate the Energy used as the primary readout during optimization
TransformationAssignMode() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
 
TransformationContext - Class in org.anchoranalysis.mpp.segment.transformer
 
TransformationContext(Dimensions, KernelCalculationContext, Logger) - Constructor for class org.anchoranalysis.mpp.segment.transformer.TransformationContext
 
TransformingGenerator<T,​S> - Interface in org.anchoranalysis.io.generator
Performs preprocessing to transform the element into another type before being written to the filesystem.
TransformingGeneratorBridge<S,​T,​V> - Class in org.anchoranalysis.io.generator
Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.
TransformingGeneratorBridge(TransformingGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.io.generator.TransformingGeneratorBridge
 
TransformMapOptional<W,​X> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
 
TransformMapOptional(StateTransformer<W, X>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformMapOptional
 
transpose() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
 
TraversalResult(List<Path>, List<Path>, int) - Constructor for class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
 
traverse(Point3i, List<Point3i>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.OutlinePixelsRetriever
 
traverse(Point3i, List<Point3i>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
TraverseDirectoryForProgressReporter - Class in org.anchoranalysis.core.progress
 
TraverseDirectoryForProgressReporter.TraversalResult - Class in org.anchoranalysis.core.progress
 
traverseNotRecursive(Path, Predicate<Path>) - Static method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter
 
TraverseOutlineException - Exception in org.anchoranalysis.plugin.mpp.bean.outline
 
TraverseOutlineException(String) - Constructor for exception org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineException
 
TraverseOutlineException(String, Throwable) - Constructor for exception org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineException
 
TraverseOutlineOnImage - Class in org.anchoranalysis.plugin.mpp.bean.outline
 
TraverseOutlineOnImage() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
 
TraversePointsOnContour - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
 
TraversePointsOnContour() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
 
traverseRecursive(Path, int, Predicate<Path>, int) - Static method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter
 
trigger() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TriggerTerminationCondition
 
TriggerTerminationCondition - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination
 
TriggerTerminationCondition() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TriggerTerminationCondition
 
Tuple3d - Class in org.anchoranalysis.spatial.point
 
Tuple3d() - Constructor for class org.anchoranalysis.spatial.point.Tuple3d
 
Tuple3f - Class in org.anchoranalysis.spatial.point
 
Tuple3f() - Constructor for class org.anchoranalysis.spatial.point.Tuple3f
 
Tuple3i - Class in org.anchoranalysis.spatial.point
 
Tuple3i() - Constructor for class org.anchoranalysis.spatial.point.Tuple3i
 
twoNonOverlappingCircles(boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.FeatureInputOverlappingCircleFixture
Two object-masks of circles in different locations WITHOUT any overlap
twoOverlappingCircles(boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.FeatureInputOverlappingCircleFixture
Two object-masks of circles in different locations WITH some overlap
TwoVoxelMappingBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
Takes the two channels and creates a NEW third channel whose pixels are a function of the two channels
TwoVoxelMappingBase(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase
 
TypedEdge<V,​P> - Class in org.anchoranalysis.core.graph
An edge that exists in a graph, together with the two vertices that it conntects.
TypedEdge(P, V, V) - Constructor for class org.anchoranalysis.core.graph.TypedEdge
 
TypedValue - Class in org.anchoranalysis.core.value
 
TypedValue(double, int) - Constructor for class org.anchoranalysis.core.value.TypedValue
 
TypedValue(int) - Constructor for class org.anchoranalysis.core.value.TypedValue
 
TypedValue(String) - Constructor for class org.anchoranalysis.core.value.TypedValue
 
TypedValue(String, boolean) - Constructor for class org.anchoranalysis.core.value.TypedValue
 

U

UnaryWithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
 
UnaryWithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
 
UnaryWithMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
 
UnaryWithMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
 
UnaryWithObjectsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
 
UnaryWithObjectsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
 
UnaryWithValueBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
A ChannelProviderUnary which has a scalar value field
UnaryWithValueBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
 
UnchangingEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
TODO consider renaming to ConstantScore
UnchangingEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
 
UnchangingNumberMarks - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
TODO consider renaming to constant size
UnchangingNumberMarks() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
 
unconvertedDataType() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
 
underlyingBytes() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
An array of bytes that underlies the buffer (and can be written into a file).
UniformProposal<S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
Repeatedly propose new collections of marks and take the collection with optimal energy.
UniformProposal() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
 
UniformRandom - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
 
UniformRandom - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
 
UniformRandom() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.UniformRandom
 
UniformRandom() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
 
UniformRandomRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii
 
UniformRandomRadiiProposer() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
 
UniformRandomRadiiProposer(Bound, boolean) - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
 
union() - Method in class org.anchoranalysis.spatial.box.BoundingBox
For performing a union between this bounding-box and another
uniqueIdentifierFor(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
 
uniqueIdentifierFor(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
 
uniqueIdentifierFor(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
Generates a unique identifier for a particular input
uniqueIdentifierFor(T) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
 
uniquelyIdentifyAllProperties() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
A string that uniquely identifies all properties in the bean, but NOT friendly to humans
uniqueName() - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
A string describing this class and all its parameterization that is guaranteed to be unique for a given set of parameters
uniqueName() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
 
uniqueName() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
 
uniqueName() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
 
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
 
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
 
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
 
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
 
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
 
uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
 
unitArea() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
unitConvert() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
Converts voxelized measurements to/from physical units.
unitConvert() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
Converts voxelized measurements to/from physical units.
UnitConverter - Class in org.anchoranalysis.image.core.dimensions
Converts from voxelized units to different physical measurements of area / volume / distance.
UnitConverter - Class in org.anchoranalysis.plugin.mpp.feature.bean.unit
Converts units (distance, area, volume) to a another representation (e.g.
UnitConverter() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
 
UnitConverter(Resolution) - Constructor for class org.anchoranalysis.image.core.dimensions.UnitConverter
 
unitConvertOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
 
UnitsWithinRange<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.plugin.image.feature.bean.physical
Checks if a value lies within a range defined by units (a minimum and maximum boundary)
UnitsWithinRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
 
UnitTestCompareUtilities - Class in org.anchoranalysis.test.experiment.launcher
 
UnitValueArea - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
 
UnitValueArea() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
 
UnitValueArea(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
 
UnitValueAreaOrVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent
 
UnitValueAreaOrVolume() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueAreaOrVolume
 
UnitValueDistance - Class in org.anchoranalysis.image.bean.unitvalue.distance
 
UnitValueDistance() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
 
UnitValueException - Exception in org.anchoranalysis.image.bean.nonbean.error
 
UnitValueException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.UnitValueException
 
UnitValueException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.UnitValueException
 
UnitValueVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume
 
UnitValueVolume() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.UnitValueVolume
 
unitVolume() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
UnsignedBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive
Base class for buffers that represent an unsigned-type in the signed-equivalent-type NIO Buffer.
UnsignedBuffer(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
 
UnsignedBufferAsInt - Class in org.anchoranalysis.image.voxel.buffer.primitive
A UnsignedBuffer that exposes its internal types as int.
UnsignedBufferAsInt(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
 
unsignedByteArray(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps an existing array (encoding unsigned bytes as a signed array) as a voxel-buffer.
unsignedByteBuffer(UnsignedByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps an unsigned-byte buffer into a voxel-buffer.
UnsignedByteBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive
Wraps a ByteBuffer but automatically performs conversion to int.
UnsignedByteFromFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
 
UnsignedByteFromFloat(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
 
UnsignedByteFromUnsignedByteInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
 
UnsignedByteFromUnsignedByteInterleaving() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
 
UnsignedByteFromUnsignedByteNoInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
 
UnsignedByteFromUnsignedByteNoInterleaving() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
 
UnsignedByteFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
 
UnsignedByteFromUnsignedInt(int, boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
 
UnsignedByteFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
 
UnsignedByteFromUnsignedShort(boolean, int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
 
unsignedByteRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps an unsigned-byte buffer (represented by a NIO signed-buffer) into a voxel-buffer.
unsignedByteToInt(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
 
unsignedByteToShort(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
 
UnsignedByteVoxelType - Class in org.anchoranalysis.image.voxel.datatype
 
unsignedIntArray(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps an unsigned-int buffer into a voxel-buffer.
unsignedIntBuffer(UnsignedIntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps an unsigned-int buffer (represented by a NIO signed-buffer) into a voxel-buffer.
UnsignedIntBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive
Wraps an IntBuffer but automatically performs conversion to long.
UnsignedIntFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint
 
UnsignedIntFromUnsignedInt(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
 
unsignedIntToInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
 
unsignedIntToLong(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
 
unsignedIntToShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
 
UnsignedIntVoxelType - Class in org.anchoranalysis.image.voxel.datatype
 
unsignedShortArray(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps an existing array (encoding unsigned shorts as a signed array) as a voxel-buffer.
unsignedShortBuffer(UnsignedShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps an unsigned-short buffer into a voxel-buffer.
UnsignedShortBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive
Wraps a ShortBuffer but automatically performs conversion to int.
UnsignedShortFromSignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort
 
UnsignedShortFromSignedShort(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromSignedShort
 
UnsignedShortFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort
 
UnsignedShortFromUnsignedShort(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromUnsignedShort
 
unsignedShortRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
Wraps an unsigned-short buffer (represented by a NIO signed-buffer) into a voxel-buffer.
unsignedShortToInt(short) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
 
UnsignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype
 
UnsignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype
 
UnsignedVoxelType(int, String, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
 
UnsupportedMarkTypeException - Exception in org.anchoranalysis.mpp.mark
 
UnsupportedMarkTypeException(Exception) - Constructor for exception org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException
 
UnsupportedMarkTypeException(String) - Constructor for exception org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException
 
untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo
Iterates each voxel until a specific intensity value is found.
UpdatableBeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
Rather than checking if obj1 vs obj2 is accepted instead there's a two stage process
UpdatableMarkSet - Interface in org.anchoranalysis.mpp.mark.set
 
UpdatablePointsContainer - Class in org.anchoranalysis.mpp.bean.points.updatable
 
UpdatablePointsContainer() - Constructor for class org.anchoranalysis.mpp.bean.points.updatable.UpdatablePointsContainer
 
update() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
 
update(double) - Method in class org.anchoranalysis.core.progress.ProgressReporterMultiple
 
update(int) - Method in interface org.anchoranalysis.core.progress.ProgressReporter
 
update(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
 
update(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
 
update(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
 
update(Integer) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
 
update(Integer) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
 
update(String) - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
 
update(Point2d, Point2d, Orientation2D) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
update(T) - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelDeathPixelized
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, MarkCollection, MarkCollection) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, MarksFromPartition, MarksFromPartition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, MarksFromPartition, MarksFromPartition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelDeathPartition
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, MarksFromPartition, MarksFromPartition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
 
updateAfterAcceptance(ListUpdatableMarkSetCollection, T, T) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
If the kernel is accepted, makes the necessary changes to a ListUpdatableMarkSetCollection
updateAfterAcceptance(ListUpdatableMarkSetCollection, T, T) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
 
updateAfterMarkChange() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
 
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
updateIndex(String, int) - Method in class org.anchoranalysis.io.generator.sequence.SequenceMemory
 
updateLabeling(double) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
Update labels with the specified slack by adding the slack value for committed workers and by subtracting the slack value for committed jobs.
UpdateMarkSetException - Exception in org.anchoranalysis.mpp.mark.set
 
UpdateMarkSetException(Exception) - Constructor for exception org.anchoranalysis.mpp.mark.set.UpdateMarkSetException
 
UpdateMarkSetException(String) - Constructor for exception org.anchoranalysis.mpp.mark.set.UpdateMarkSetException
 
updateResolution(Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.Channel
 
updateResolution(Resolution) - Method in class org.anchoranalysis.image.core.stack.Stack
 
updateShellRad(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
updateSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
 
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
 
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
 
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition
 
updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
 
updateTotal(MemoCollection, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
 
UpperLowerQuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
 
UpperLowerQuantileIntensity(double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.UpperLowerQuantileIntensity
 
UpperLowerQuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram
Scales by a lower and upper quantile of the intensity values of an image
UpperLowerQuantileIntensityFromHistogram(double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
 
UpperLowerQuantileIntensityFromHistogram(double, double, double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
 
useDefault() - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
Use default manager.
UseDefaultManager - Class in org.anchoranalysis.launcher.executor.selectparam
Uses whatever default-manager exists
UseDefaultManager() - Constructor for class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
 
useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.Experiment
Whether to detail more (a lengthy experiment) or less (something quick and simple - suitable for console)?
useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
 
useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
 
useDetailedLogging() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
 
useDetailedLogging() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
 
useDetailedLogging() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
 
useDetailedLogging() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
 
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
Uses calculateLevelElse instead of the standard calculation-level approach
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
 
useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
 
useZ - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
 

V

valueByDimension(int) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
valueByDimension(int) - Method in class org.anchoranalysis.spatial.Extent
 
valueByDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
valueByDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
valueByDimension(AxisType) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
valueByDimension(AxisType) - Method in class org.anchoranalysis.spatial.Extent
 
valueByDimension(AxisType) - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
valueByDimension(AxisType) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
valueFor(SessionInput<FeatureInputSingleObject>, ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
 
valueFor(SessionInput<FeatureInputSingleObject>, ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
 
valueFor(SessionInput<FeatureInputSingleObject>, ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
 
valueFor(AxisType, int, int, int) - Static method in class org.anchoranalysis.spatial.axis.AxisTypeConverter
Multiplexes the correct value for the given dimension
valueFromFirst(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
valueFromMerged(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
valueFromSecond(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
 
valueOf(String) - Static method in enum org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.image.core.channel.convert.ConversionPolicy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.spatial.axis.AxisType
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.image.core.channel.convert.ConversionPolicy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.spatial.axis.AxisType
Returns an array containing the constants of this enum type, in the order they are declared.
variance() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
 
variance() - Method in class org.anchoranalysis.math.histogram.Histogram
 
variance() - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
Calculate the variance
Variance - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
 
Variance() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
 
VarianceCalculator - Class in org.anchoranalysis.math.statistics
Helper class for calculating variance from running variables
VarianceCalculator() - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculator
 
VarianceCalculator(long, long, long) - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculator
 
VarianceFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
 
VarianceFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.VarianceFilter2D
 
Vector3d - Class in org.anchoranalysis.spatial.point
 
Vector3d() - Constructor for class org.anchoranalysis.spatial.point.Vector3d
 
Vector3d(double, double, double) - Constructor for class org.anchoranalysis.spatial.point.Vector3d
 
Vector3d(Tuple3d) - Constructor for class org.anchoranalysis.spatial.point.Vector3d
 
VectorInDirection - Class in org.anchoranalysis.image.bean.spatial.direction
 
VectorInDirection() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
VectorInDirection(double, double, double) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
VectorInDirection(DirectionVector) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
 
verifySeedsAreInside(Extent) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
 
vertices() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
The set of all vertices in the graph.
verticesAsObjects() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
 
VeryBright - Class in org.anchoranalysis.bean.shared.color.scheme
Creates a list by repeating a defined list of very bright colors.
VeryBright() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.VeryBright
 
VisitedVoxels - Class in org.anchoranalysis.image.core.outline.traverser.visited
All pixels that have been visited so far
VisitedVoxels() - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
 
VisitScheduler - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
 
VisitScheduler() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
 
VisitSchedulerAnd - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
 
VisitSchedulerAnd() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
 
VisitSchedulerConvexAboutRoot - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
 
VisitSchedulerConvexAboutRoot() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
 
VisitSchedulerMaxDistanceAlongContour - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
 
VisitSchedulerMaxDistanceAlongContour() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
 
VisitSchedulerUniformSample - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
 
VisitSchedulerUniformSample() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
 
visualization() - Method in interface org.anchoranalysis.mpp.probmap.ProbMap
 
visualization() - Method in class org.anchoranalysis.mpp.probmap.ProbMapObjects
 
VisualizeOnBackground - Class in org.anchoranalysis.plugin.mpp.bean.define
Adds a visualization for all binary-masks and object-collections that are added using a particular background
VisualizeOnBackground() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Circle
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.Mark
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PointList
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
 
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
 
Volume<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
Calculates the volume (x, y and z dimensions) of the scene from the dimensions
Volume - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
 
Volume() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
 
Volume() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.Volume
 
volumeAgg(VoxelizedMarkMemo, VoxelizedMarkMemo, int, RelationBean, LongBinaryOperator) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
 
VolumeMin - Class in org.anchoranalysis.plugin.mpp.bean.check
 
VolumeMin() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
 
VolumePhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume
 
VolumePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
 
volumeStatistic(VoxelizedMarkMemo, VoxelizedMarkMemo, int, RelationBean, LongBinaryOperator) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
 
VolumeVoxels - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume
 
VolumeVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
 
VolumeVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
 
volumeXY() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
volumeXY() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
How many pixels in an XY slice
volumeXY() - Method in class org.anchoranalysis.spatial.Extent
 
voxel(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
voxel(ReadableTuple3i) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
Gets the value of one particular value
voxelAtBufferIndex(T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
VoxelBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer
A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
VoxelBuffer() - Constructor for class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
 
VoxelBufferFactory - Class in org.anchoranalysis.image.voxel.buffer
Creating voxel-buffers and arrays of voxel-buffers of various types.
VoxelBufferWrap - Class in org.anchoranalysis.image.voxel.buffer
Wraps arrays and buffers of primitive-types into VoxelBuffer.
VoxelDataType - Class in org.anchoranalysis.image.voxel.datatype
The type of data one voxel represents in an image-channel.
VoxelDataType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataType
 
VoxelDataTypeFactoryMultiplexer<T> - Class in org.anchoranalysis.image.voxel.datatype
Multiplexes between factories for the various VoxelDataTypes.
VoxelDataTypeFactoryMultiplexer(T, T, T, T) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer
 
voxelized() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
A voxelized-respentation of the mark
VoxelizedMark - Interface in org.anchoranalysis.mpp.mark.voxelized
A voxelized representation of a Mark i.e.
VoxelizedMarkFactory - Class in org.anchoranalysis.mpp.mark.voxelized
 
VoxelizedMarkMemo - Class in org.anchoranalysis.mpp.mark.voxelized.memo
Memoization of retrieving a VoxelizedMark from a mark
VoxelizedMarkMemo(Mark, EnergyStackWithoutParams, RegionMap) - Constructor for class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
 
VoxelizedMarksChangeReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
VoxelizedMarksChangeReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
 
VoxelizedMarksPeriodicReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
 
VoxelizedMarksPeriodicReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
 
VoxelizedMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks
A collection of marks, their voxelized equivalents, and associated energy.
VoxelizedMarksWithEnergy(MarksWithEnergyBreakdown, EnergyStack, SharedFeatureMulti, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
 
VoxelizedMarksWithEnergyFactory - Class in org.anchoranalysis.plugin.mpp.segment.optimization
 
VoxelizeWithTransform<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
Converts a Marks to a MarksToPixelized using a transformer
VoxelizeWithTransform() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
 
VoxelizeWithTransform(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
 
VoxelPartition<T> - Interface in org.anchoranalysis.mpp.voxel.partition
A partition of voxels
VoxelPartitionFactory<T> - Interface in org.anchoranalysis.mpp.voxel.partition.factory
 
VoxelPartitionFactoryHistogramReuse - Class in org.anchoranalysis.mpp.voxel.partition.factory
 
VoxelPartitionFactoryHistogramReuse() - Constructor for class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactoryHistogramReuse
 
VoxelPartitionHistogram - Class in org.anchoranalysis.mpp.voxel.partition
 
VoxelPartitionHistogram(int, Supplier<Histogram>) - Constructor for class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
 
VoxelPartitonFactoryHistogram - Class in org.anchoranalysis.mpp.voxel.partition.factory
 
VoxelPartitonFactoryHistogram() - Constructor for class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitonFactoryHistogram
 
VoxelPhysicalSize<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
The physical size of a pixel in a specific dimension.
VoxelPhysicalSize() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize
 
voxels - Variable in class org.anchoranalysis.image.voxel.extracter.Base
The voxels to extract from
voxels() - Method in class org.anchoranalysis.image.core.channel.Channel
 
voxels() - Method in class org.anchoranalysis.image.core.mask.Mask
 
voxels() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
Voxels that should only have two intensity-values (representing ON and OFF states).
voxels() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
Voxel-data that fits inside the bounding-box (its extent is invariant with the extent of the bounding-box).
voxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
voxels() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
 
voxels() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
 
Voxels<T> - Class in org.anchoranalysis.image.voxel
A box (3-dimensions) with voxel-data.
Voxels(SliceBufferIndex<T>, VoxelsFactoryTypeBound<T>, VoxelsArithmetic) - Constructor for class org.anchoranalysis.image.voxel.Voxels
 
VoxelsArithmetic - Interface in org.anchoranalysis.image.voxel.arithmetic
 
VoxelsArithmeticFactory - Class in org.anchoranalysis.image.voxel.arithmetic
 
VoxelsAsFloat - Class in org.anchoranalysis.image.voxel
 
VoxelsAsFloat(SliceBufferIndex<FloatBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsAsFloat
 
VoxelsAsInt - Class in org.anchoranalysis.image.voxel
 
VoxelsAsInt(SliceBufferIndex<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsAsInt
 
VoxelsAsShort - Class in org.anchoranalysis.image.voxel
 
VoxelsAsShort(SliceBufferIndex<UnsignedShortBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsAsShort
 
VoxelsAssigner - Interface in org.anchoranalysis.image.voxel.assigner
Assigns values to some or all voxels
VoxelsAssignerFactory - Class in org.anchoranalysis.image.voxel.assigner
 
VoxelsConverter<T> - Class in org.anchoranalysis.image.voxel.convert
Converts voxels from one data-type to another.
VoxelsConverter() - Constructor for class org.anchoranalysis.image.voxel.convert.VoxelsConverter
 
VoxelScore - Class in org.anchoranalysis.image.feature.bean.score
Calculates a per-voxel score
VoxelScore() - Constructor for class org.anchoranalysis.image.feature.bean.score.VoxelScore
 
voxelsEqualTo(int) - Method in class org.anchoranalysis.image.core.channel.Channel
Operations on whether particular voxels are equal to a particular value
voxelsEqualTo(int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
voxelsEqualTo(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
Operations on whether particular voxels are equal to a particular value
VoxelsExtracter<T> - Interface in org.anchoranalysis.image.voxel.extracter
Provides method to read/copy/duplicate portions of voxels
VoxelsExtracterFactory - Class in org.anchoranalysis.image.voxel.extracter
 
VoxelsFactory - Class in org.anchoranalysis.image.voxel.factory
 
VoxelsFactoryTypeBound<T> - Interface in org.anchoranalysis.image.voxel.factory
A factory for creating voxels with a particular buffer-type
voxelsGreaterThan(int) - Method in class org.anchoranalysis.image.core.channel.Channel
Operations on whether particular voxels are greater than a treshold (but not equal to)
voxelsGreaterThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
 
voxelsGreaterThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
Operations on whether particular voxels are greater than a treshold (but not equal to)
voxelsMaximumIntensityProjection() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
 
voxelsOff() - Method in class org.anchoranalysis.image.core.mask.Mask
 
voxelsOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
voxelsOn() - Method in class org.anchoranalysis.image.core.mask.Mask
 
voxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
 
VoxelsPredicate - Interface in org.anchoranalysis.image.voxel.extracter.predicate
Methods to find or count voxels that satisfy a predicate.
VoxelStatistics - Interface in org.anchoranalysis.image.voxel.statistics
Allows retrieval of statistics about voxel intensities.
VoxelStatisticsCombined - Class in org.anchoranalysis.image.voxel.statistics
 
VoxelStatisticsCombined() - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
 
VoxelStatisticsFromHistogram - Class in org.anchoranalysis.image.voxel.statistics
 
VoxelStatisticsFromHistogram(Histogram) - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
 
VoxelsThresholder - Class in org.anchoranalysis.image.voxel.thresholder
Performs threshold operation on voxels.
VoxelsUnsignedByte - Class in org.anchoranalysis.image.voxel
 
VoxelsUnsignedByte(SliceBufferIndex<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
 
VoxelsWrapper - Class in org.anchoranalysis.image.voxel
Wraps a voxels associated with a channel so it can be easily casted to an appropriate data type
VoxelsWrapper(Voxels<?>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsWrapper
 
VoxelsWrapperList - Class in org.anchoranalysis.image.voxel
 
VoxelsWrapperList() - Constructor for class org.anchoranalysis.image.voxel.VoxelsWrapperList
 
voxelWithMaxIntensity() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
Finds the maximum-value of any voxel and rounds up (ceiling) to nearest long

W

WatershedEncoding - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
 
WatershedEncoding() - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
 
WatershedYeong - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
A 'rainfall' watershed algorithm
WatershedYeong() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
 
WeightedKernel<T> - Class in org.anchoranalysis.mpp.segment.kernel.proposer
A kernel with an associated weight.
WeightedKernel(Kernel<T>, double) - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
Constructor for single kernel factory
WeightedKernelList<T> - Class in org.anchoranalysis.mpp.segment.kernel.proposer
 
WeightedKernelList() - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
 
weightFor(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ConstantWeight
 
weightFor(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ExtractWeightFromMark
 
weightFor(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.NumberPoints
 
weightWidthDescription() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
 
weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
 
weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
 
WholeImageLabelAnnotationReader - Class in org.anchoranalysis.annotation.io.image
 
WholeImageLabelAnnotationReader() - Constructor for class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationReader
 
WholeImageLabelAnnotationWriter - Class in org.anchoranalysis.annotation.io.image
 
WholeImageLabelAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationWriter
 
WholeImageLabelStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
 
WholeImageLabelStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
 
with(Feature<T>, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
Starts a feature-session for a single feature
with(Feature<T>, FeatureInitParams, SharedFeatureMulti, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
 
with(Feature<T>, SharedFeatureMulti, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
Starts a feature-session for a single feature
with(FeatureList<T>, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
Starts a feature-session for a list of features
with(FeatureList<T>, FeatureInitParams, Optional<SharedFeatureMulti>, Logger, BoundReplaceStrategy<T, ? extends ReplaceStrategy<T>>) - Static method in class org.anchoranalysis.feature.session.FeatureSession
 
with(FeatureList<T>, FeatureInitParams, SharedFeatureMulti, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
 
with(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection
 
with(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxUnion
Performs a union with another box (immutably)
withBuffer(Optional<ObjectMask>, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional
Iterate over each voxel on an object-mask with one associated buffer.
withBuffer(Mask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.core.mask.IterateVoxelsMask
Iterate over each voxel in a mask - with an associated buffer for each slice from a voxel-bo
withBuffer(ObjectMask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
Iterate over each voxel in an object-mask - with one associated buffer for each slice from Voxels.
withBuffer(Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Iterate over each voxel - with one associated buffer for each slice.
withBuffer(BoundingBox, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
Iterate over each voxel in a bounding-box - with one associated buffer for each slice
withCalculateLevel(Histogram, CalculateLevel) - Static method in class org.anchoranalysis.plugin.image.intensity.HistogramThresholder
Retains the portion of the histogram greater or equal to the calculated-level
WithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
 
WithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
 
WithConfidence<T> - Class in org.anchoranalysis.plugin.image.segment
Wraps an element with a confidence-score and imposes an ordering (highest confidence first).
WithConfidence(T, double) - Constructor for class org.anchoranalysis.plugin.image.segment.WithConfidence
 
WithContainerBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
Base class for ObjectCollectionProvider that take an optional objectsContainer bean-field.
WithContainerBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
 
WithDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
Base class for ObjectCollectionProviderUnary classes that require dimensions to be specified.
WithDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
 
within(Optional<ObjectMask>, Extent, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
Within either an object-mask or an extent (as a fallback)
withinExtent(ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
 
withinMask(ObjectMask, ProcessChangedPointAbsoluteMasked<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
 
withinMask(ObjectMask, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
 
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
 
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
 
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
 
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
 
withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
What value to return if the value is inside the range
withInside(BoundingBox, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection
Find the intersection and clip to a a containing extent
withLabel(String) - Method in class org.anchoranalysis.experiment.log.Divider
Creates a line of repeated dashes with a centered label of text.
withMatchingPoints(BoundingBox, Predicate<Point3i>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
Iterate over each voxel in a bounding-box that matches a predicate.
WithOptionalDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
Base class for ObjectCollectionProviderUnary classes that offer an optional means to specify dimensions.
WithOptionalDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
 
withoutColor() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
 
withoutLabel() - Method in class org.anchoranalysis.experiment.log.Divider
Creates a line of repeated dashes.
withoutOrder(OutputPatternStringSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
Writes elements (indexed by strings) to directory, without any order in the sequence.
withoutOrderCurrentDirectory(String) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
Writes elements (indexed by strings) to the current directory, without any order in the sequence.
withoutParams() - Method in class org.anchoranalysis.feature.energy.EnergyStack
The energy-stack without associated parameters.
withoutProgressReporter() - Method in interface org.anchoranalysis.core.progress.CheckedProgressingSupplier
 
withoutProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
Returns the contained-objects without corresponding properties
withoutProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
 
withoutUniformSizeConstraint() - Method in class org.anchoranalysis.image.core.stack.NamedStacksUniformSize
 
withPoint(Optional<ObjectMask>, Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional
Iterate over all points that are located on a object-mask or else all points in an extent.
withPoint(ObjectMask, Optional<ObjectMask>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
Iterate over each point that is located on an object-mask AND optionally a second-mask
withPoint(ObjectMask, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
Iterate over each voxel that is located on an object-mask
withPoint(BoundingBox, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
Iterate over each voxel in a bounding-box
withPoint(Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Iterate over each voxel in an Extent
WithPriority<T> - Class in org.anchoranalysis.core.concurrency
 
WithPriority(T, boolean) - Constructor for class org.anchoranalysis.core.concurrency.WithPriority
 
WithRadiusBase - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider
A ChannelProviderUnary with a 'radius' parameter
WithRadiusBase() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
 
WithResolutionBase<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
 
WithResolutionBase() - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
 
WithResolutionBase(Feature<T>) - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
 
withSlidingBuffer(Optional<ObjectMask>, SlidingBuffer<?>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional
Iterate over each voxel in a sliding-buffer, optionally restricting it to be only voxels in a certain object
withThreeBuffers(Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Iterate over each voxel - with three associated buffers for each slice.
withThreeBuffers(BoundingBox, ReadableTuple3i, ReadableTuple3i, Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
Iterate over each voxel in a bounding-box - with three associated buffers for each slice.
withTwoBuffers(BoundedVoxels<T>, BoundedVoxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded
Iterates over the intersection of two bounded-voxels of type BoundedVoxels.
withTwoBuffers(ObjectMask, Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
Iterate over each voxel with a corresponding ON value in an object-mask - and with two associated buffers for each slice covering the all the global space i.e.
withTwoBuffers(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, ProcessBufferBinary<UnsignedByteBuffer, UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded
Iterates over the intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask.
withTwoBuffers(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
Iterate over each voxel in a bounding-box - with two associated buffers for each slice, one VoxelBuffer and one Buffer
withTwoBuffersAndPoint(Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Iterate over each voxel - with two associated buffers for each slice
withTwoBuffersUntil(BoundedVoxels<T>, BoundedVoxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded
Iterates over the intersection of two bounded-voxels of type BoundedVoxels until a predicate is satisfied.
withTwoBuffersUntil(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
Iterate over each voxel in a bounding-box - with two associated buffers for each slice - until a predicate evaluates to true.
withTwoBuffersWithoutOffset(VoxelBuffer<S>, VoxelBuffer<T>, ProcessBufferBinaryWithoutOffset<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsRemaining
Iterate over remaining voxels each voxel - with two associated buffers for each slice.
withTwoMixedBuffers(BoundingBox, ReadableTuple3i, Voxels<S>, Voxels<T>, ProcessBufferBinaryMixed<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
Iterate over each voxel in a bounding-box - with two associated buffers for each slice.
withTwoVoxelBuffers(Voxels<S>, Voxels<T>, ProcessVoxelBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Iterate over each voxel in a bounding-box - with two associated voxel-buffers for each slice
WithValueBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean
Operations that use a specified constant value
WithValueBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
 
withVoxelBuffer(ObjectMask, Voxels<T>, Optional<BoundingBox>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
Iterate over each voxel on an object-mask with one associated VoxelBuffer.
withVoxelBuffer(ObjectMask, Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
Iterate over each voxel on an object-mask with one associated VoxelBuffer.
withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Iterate over each voxel - with one associated voxel-buffer for each slice.
withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnaryWithPoint<T, E>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
Iterate over each voxel - with one associated voxel-buffer for each slice.
wrap(String, Throwable) - Static method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
 
wrap(Voxels<?>) - Static method in class org.anchoranalysis.image.voxel.VoxelsWrapper
 
Wrap - Class in org.anchoranalysis.image.voxel.convert.imglib2
 
WrapAbsoluteAsMasked<T> - Class in org.anchoranalysis.image.voxel.iterator.neighbor
WrapAbsoluteAsMasked(ProcessVoxelNeighborAbsolute<T>) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
 
WrapAsUpdatable - Class in org.anchoranalysis.plugin.image.object.merge.condition
Wraps a BeforeCondition as an UpdatableBefoerCondition
WrapAsUpdatable(BeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
 
wrapDuplicate(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Wraps an existing list, WITHOUT reusing the list in the internals of the FeatureList i.e.
wrapRaw(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Exposes a raw byte-array as a buffer with unsigned-bytes.
wrapRaw(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Exposes a raw int-array as a buffer with unsigned-ints.
wrapRaw(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Exposes a raw short-array as a buffer with unsigned-shorts.
wrapRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
Exposes a raw ByteBuffer as a buffer with unsigned-bytes.
wrapRaw(IntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
Exposes a raw UnsignedIntBuffer as a buffer with unsigned-ints.
wrapRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
Exposes a raw UnsignedShortBuffer as a buffer with unsigned-shorts.
wrapReuse(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
Wraps an existing list, reusing the list in the internals of the FeatureList
WrapStackAsTimeSequence - Class in org.anchoranalysis.image.core.stack.wrap
 
WrapStackAsTimeSequence(NamedProvider<Stack>) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequence
 
WrapStackAsTimeSequenceStore - Class in org.anchoranalysis.image.core.stack.wrap
 
WrapStackAsTimeSequenceStore(NamedProviderStore<Stack>) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
 
WrapStackAsTimeSequenceStore(NamedProviderStore<Stack>, int) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
 
WrapTimeSequenceAsStack - Class in org.anchoranalysis.image.core.stack.wrap
 
WrapTimeSequenceAsStack(NamedProvider<TimeSequence>) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapTimeSequenceAsStack
 
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
 
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
 
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in interface org.anchoranalysis.io.output.writer.Writer
Writes an element using an ElementWriter to the current directory.
write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors
Writes an element using an ElementWriter to the current directory.
write(Collection<T>, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
 
write(ImageLabelAnnotation, Path) - Method in class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationWriter
 
write(DualMarksAnnotation<T>, Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
 
write(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes) - Method in class org.anchoranalysis.overlay.bean.DrawObject
 
write(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.overlay.bean.DrawObject
 
write(Manifest, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.ManifestGenerator
 
write(S, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.GeneratorBridge
 
write(T, Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationWriter
Saves the annotation to the filesystem
write(T, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
 
write(T, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
 
write(T, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
 
write(T, OutputNameStyle, OutputterChecked) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter
Writes a non-indexable output (an output that isn't part of a collection of other similar items)
writeEnergyStack() - Method in class org.anchoranalysis.mpp.io.output.EnergyStackWriter
 
writeFeaturesToCSV(CSVWriter, List<ImageAnnotation>, List<String>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator
 
writeFeaturesToCSV(CSVWriter, ResultsVectorList, List<String>) - Method in class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorHorizontal
 
writeFeaturesToCSV(CSVWriter, ResultsVectorList, List<String>) - Method in class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorVertical
 
writeFeaturesToCSV(CSVWriter, T, List<String>) - Method in class org.anchoranalysis.feature.io.csv.FeatureTableCSVGenerator
Writes the features to the CSV-file.
writeFileToOperationRecorder(String, Path, ManifestDescription, String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
Writes a file-entry to the operation recorder
writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
Writes all the results that have been collected as a CSV file.
writeGroupOutputInSubdirectory(String, T, ConsistentChannelChecker, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
 
writeGroupResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, InputOutputContext, InputOutputContextSubdirectoryCache) - Method in class org.anchoranalysis.feature.io.results.group.GroupWriter
writeHeaders(List<String>) - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
 
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
Creates a channel with the levels for a set of objects
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
 
writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
 
writeOffByte(int, UnsignedByteBuffer) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
 
WriteOperationRecorder - Interface in org.anchoranalysis.io.manifest.operationrecorder
Makes a record of an output written to the filesystem.
writeOverlays(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
Writes a collection of colored-overlays to the background
writeOverlaysIfIntersects(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>, List<BoundingBox>) - Method in class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
 
writeOverlaysIfIntersects(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>, List<BoundingBox>) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
 
writePrecalculatedMask(RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.overlay.writer.PrecalculationOverlay
 
writePrecalculatedOverlays(List<PrecalculationOverlay>, Dimensions, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
 
writePrecalculatedOverlays(List<PrecalculationOverlay>, Dimensions, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
 
Writer - Interface in org.anchoranalysis.io.output.writer
Write data via ElementWriters to the file system, or creates new sub-directories for writing data to.
writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
Writes an annotation to the filesystem at outPath.
writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
 
writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
 
writeResolutionXml(Resolution, Path) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXml
Writes a XML metadata file describing the image-resolution.
WriteResolutionXml - Class in org.anchoranalysis.plugin.io.bean.stack.writer
When writing a stack, an additional file is written to indicate the physical voxel sizes, if this information is known.
WriteResolutionXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
 
writeResultsForAllGroups(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, InputOutputContext) - Method in class org.anchoranalysis.feature.io.results.ResultsWriter
Writes the stored-results to CSV files.
WriterExecuteBeforeEveryOperation - Interface in org.anchoranalysis.io.output.writer
 
writeRGBColorToByteArray(RGBColor, Point3i, Dimensions, UnsignedByteBuffer, UnsignedByteBuffer, UnsignedByteBuffer) - Static method in class org.anchoranalysis.image.core.stack.rgb.RGBOutputUtils
 
writeRGBMaskToSlice(ObjectMask, BoundingBox, RGBColor, Point3i, int, ReadableTuple3i) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
writeRGBPoint(Point3i, RGBColor) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
 
writerMultiplex(boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter
Multiplexes between the selective and permissive writers based on a flag.
writeRow(String, int, double) - Method in class org.anchoranalysis.plugin.image.task.slice.SharedStateSelectedSlice
 
writeRow(String, String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
 
writeRow(List<TypedValue>) - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
 
writerPermissive() - Method in class org.anchoranalysis.io.output.outputter.Outputter
The writer that allows all outputs.
WriterRouterErrors - Class in org.anchoranalysis.io.output.writer
Write data via ElementWriters to the file system, or creates new sub-directories for writng data to.
WriterRouterErrors(Writer, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.writer.WriterRouterErrors
 
writers() - Method in interface org.anchoranalysis.io.generator.sequence.OutputSequence
 
writers() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
 
writers() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
 
writerSecondLevel(String) - Method in class org.anchoranalysis.io.output.outputter.Outputter
A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
writerSelective() - Method in class org.anchoranalysis.io.output.outputter.Outputter
The writer that allows only certain selected outputs.
WriterUtilities - Class in org.anchoranalysis.annotation.io
 
writeSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.overlay.bean.DrawObject
Draws a single-object on top of a RGB-stack
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
 
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
 
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
 
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
 
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
 
writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter
 
writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.plugin.opencv.bean.writer.OpenCVWriter
 
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.NoTimeSeries
 
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.SupportsTimeSeries
 
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
 
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
 
writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
 
writeStackTime(Stack, Path, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
Writes a stack as a time-sequence (many images together in a single file.).
WriteStringToFile - Class in org.anchoranalysis.io.generator.text
 
writeThresholdedByte(int, UnsignedByteBuffer, VoxelBuffer<?>, VoxelBuffer<?>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
 
writeToFile(String, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.text.StringGenerator
 
writeToFile(Path) - Method in class org.anchoranalysis.core.value.KeyValueParams
Serializes the key-value params to a file
writeToFile(KeyValueParams, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
 
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.feature.io.csv.FeatureTableCSVGenerator
 
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
 
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.XStreamGenerator
 
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
 
writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
 
writeToXML(CSVRow, Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
 
writeToXML(CSVRow, Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
 
writeToXML(CSVRow, Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
 
writeToXML(Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
 
writeWithIndex(Collection<T>, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
 
writeWithIndex(Manifest, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.ManifestGenerator
 
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
 
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
 
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in interface org.anchoranalysis.io.output.writer.Writer
Writes an indexed-element using an ElementWriter in the current directory.
writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors
Writes an indexed-element using an ElementWriter in the current directory.
writeWithIndex(S, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.GeneratorBridge
 
writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
 
writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
 
writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
 
writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter
Writes an indexable output (many outputs of the same type, uniquely identified by an index)
writeXmlToFile(Document, Path) - Static method in class org.anchoranalysis.io.output.xml.XMLWriter
Writes a XML-document to the file-system.

X

x - Variable in class org.anchoranalysis.spatial.point.Tuple3d
 
x - Variable in class org.anchoranalysis.spatial.point.Tuple3f
 
x - Variable in class org.anchoranalysis.spatial.point.Tuple3i
 
x() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
x() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
x() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
 
x() - Method in class org.anchoranalysis.spatial.Extent
 
x() - Method in class org.anchoranalysis.spatial.point.Point2d
 
x() - Method in class org.anchoranalysis.spatial.point.Point2f
 
x() - Method in class org.anchoranalysis.spatial.point.Point2i
 
x() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
 
x() - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
x() - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
x() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
x() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
 
x(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
x(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
Is this value in the x-dimension within the bounding box range?
X - org.anchoranalysis.spatial.axis.AxisType
 
X_Y_ONLY - org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
The dilation applies in X and Y -dimensions only, and not in Z-dimension.
xFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
 
XMLGenerator<T> - Class in org.anchoranalysis.io.generator.xml
 
XMLGenerator() - Constructor for class org.anchoranalysis.io.generator.xml.XMLGenerator
 
XmlUtilities - Class in org.anchoranalysis.bean.xml
 
XMLWriter - Class in org.anchoranalysis.io.output.xml
 
Xor - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.
Xor() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor
 
XStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize
Deserializes an object using the XStream library.
XStreamDeserializer() - Constructor for class org.anchoranalysis.core.serialize.XStreamDeserializer
 
XStreamGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
 
XStreamGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.XStreamGenerator
 
XStreamGenerator(Optional<String>) - Constructor for class org.anchoranalysis.io.generator.serialized.XStreamGenerator
 
XStreamSerializer - Class in org.anchoranalysis.core.serialize
Serializes an object using the XStream library.
XYOrientationExtendToZ - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points
 
XYOrientationExtendToZ() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
 

Y

y - Variable in class org.anchoranalysis.spatial.point.Tuple3d
 
y - Variable in class org.anchoranalysis.spatial.point.Tuple3f
 
y - Variable in class org.anchoranalysis.spatial.point.Tuple3i
 
y() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
y() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
y() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
 
y() - Method in class org.anchoranalysis.spatial.Extent
 
y() - Method in class org.anchoranalysis.spatial.point.Point2d
 
y() - Method in class org.anchoranalysis.spatial.point.Point2f
 
y() - Method in class org.anchoranalysis.spatial.point.Point2i
 
y() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
 
y() - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
y() - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
y() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
y() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
 
y(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
y(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
Is this value in the y-dimension within the bounding box range?
Y - org.anchoranalysis.spatial.axis.AxisType
 
yFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
 

Z

z - Variable in class org.anchoranalysis.spatial.point.Tuple3d
 
z - Variable in class org.anchoranalysis.spatial.point.Tuple3f
 
z - Variable in class org.anchoranalysis.spatial.point.Tuple3i
 
z() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
 
z() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
 
z() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
 
z() - Method in class org.anchoranalysis.spatial.Extent
 
z() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
 
z() - Method in class org.anchoranalysis.spatial.point.Tuple3d
 
z() - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
z() - Method in class org.anchoranalysis.spatial.point.Tuple3i
 
z(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
 
z(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
Is this value in the z-dimension within the bounding box range?
Z - org.anchoranalysis.spatial.axis.AxisType
 
Z_ONLY - org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
The dilation applies only in the Z-dimension.
zChange - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
 
ZeroOutsideMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
ZeroOutsideMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
 
zeroValue(int) - Method in class org.anchoranalysis.math.histogram.Histogram
 
zFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
 
zRelative() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
Assumes x and y has constant resolution, and gives the relative resolution of z to x or y.
zScore(double) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
 
ZScore<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.score
 
ZScore() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.score.ZScore
 
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